step.03_prepare_for_step.04.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 选取rawcounts矩阵以及计算RPKM进行筛选\n",
    "https://github.com/reneshbedre/bioinfokit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from bioinfokit.analys import norm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "ordered_bam_labels = [\n",
    "    'Geneid',\n",
    "    'Length',\n",
    "    \"CTCF_AID_auxin1day_rep1\",\n",
    "    \"CTCF_AID_auxin1day_rep2\",\n",
    "    \"CTCF_AID_auxin1day_rep3\",\n",
    "    \"CTCF_AID_auxin2days_rep1\",\n",
    "    \"CTCF_AID_auxin2days_rep2\",\n",
    "    \"CTCF_AID_auxin2days_rep3\",\n",
    "    \"CTCF_AID_auxin4days_rep1\",\n",
    "    \"CTCF_AID_auxin4days_rep2\",\n",
    "    \"CTCF_AID_auxin4days_rep3\",\n",
    "    \"CTCF_AID_untreated_rep1\",\n",
    "    \"CTCF_AID_untreated_rep2\",\n",
    "    \"CTCF_AID_untreated_rep3\",\n",
    "    \"CTCF_AID_washoff2days_rep1\",\n",
    "    \"CTCF_AID_washoff2days_rep2\",\n",
    "    \"CTCF_AID_washoff2days_rep3\",\n",
    "    \"WT_untagged_auxin2days_rep1\",\n",
    "    \"WT_untagged_auxin2days_rep2\",\n",
    "    \"WT_untagged_auxin2days_rep3\",\n",
    "    \"WT_untagged_auxin4days_rep1\",\n",
    "    \"WT_untagged_auxin4days_rep2\",\n",
    "    \"WT_untagged_auxin4days_rep3\",\n",
    "    \"WT_untagged_untreated_rep1\",\n",
    "    \"WT_untagged_untreated_rep2\",\n",
    "    \"WT_untagged_untreated_rep3\"\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Geneid</th>\n",
       "      <th>Length</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin1day_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin1day_rep2_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin1day_rep3_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin2days_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin2days_rep2_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin2days_rep3_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin4days_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_auxin4days_rep2_Aligned.out.bam</th>\n",
       "      <th>...</th>\n",
       "      <th>../bam/RNA-seq_CTCF-AID_washoff2days_rep3_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin2days_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin2days_rep2_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin2days_rep3_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin4days_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin4days_rep2_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_auxin4days_rep3_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_untreated_rep1_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_untreated_rep2_Aligned.out.bam</th>\n",
       "      <th>../bam/RNA-seq_WT-untagged_untreated_rep3_Aligned.out.bam</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ENSMUSG00000102693.1</td>\n",
       "      <td>1070</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ENSMUSG00000064842.1</td>\n",
       "      <td>110</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 Geneid  Length  \\\n",
       "0  ENSMUSG00000102693.1    1070   \n",
       "1  ENSMUSG00000064842.1     110   \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin1day_rep1_Aligned.out.bam  \\\n",
       "0                                                  0        \n",
       "1                                                  0        \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin1day_rep2_Aligned.out.bam  \\\n",
       "0                                                  0        \n",
       "1                                                  0        \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin1day_rep3_Aligned.out.bam  \\\n",
       "0                                                  0        \n",
       "1                                                  0        \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin2days_rep1_Aligned.out.bam  \\\n",
       "0                                                  0         \n",
       "1                                                  0         \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin2days_rep2_Aligned.out.bam  \\\n",
       "0                                                  0         \n",
       "1                                                  0         \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin2days_rep3_Aligned.out.bam  \\\n",
       "0                                                  0         \n",
       "1                                                  0         \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin4days_rep1_Aligned.out.bam  \\\n",
       "0                                                  0         \n",
       "1                                                  0         \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_auxin4days_rep2_Aligned.out.bam  ...  \\\n",
       "0                                                  0        ...   \n",
       "1                                                  0        ...   \n",
       "\n",
       "   ../bam/RNA-seq_CTCF-AID_washoff2days_rep3_Aligned.out.bam  \\\n",
       "0                                                  0           \n",
       "1                                                  0           \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin2days_rep1_Aligned.out.bam  \\\n",
       "0                                                  0            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin2days_rep2_Aligned.out.bam  \\\n",
       "0                                                  0            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin2days_rep3_Aligned.out.bam  \\\n",
       "0                                                  0            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin4days_rep1_Aligned.out.bam  \\\n",
       "0                                                  0            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin4days_rep2_Aligned.out.bam  \\\n",
       "0                                                  3            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_auxin4days_rep3_Aligned.out.bam  \\\n",
       "0                                                  0            \n",
       "1                                                  0            \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_untreated_rep1_Aligned.out.bam  \\\n",
       "0                                                  0           \n",
       "1                                                  0           \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_untreated_rep2_Aligned.out.bam  \\\n",
       "0                                                  1           \n",
       "1                                                  0           \n",
       "\n",
       "   ../bam/RNA-seq_WT-untagged_untreated_rep3_Aligned.out.bam  \n",
       "0                                                  0          \n",
       "1                                                  0          \n",
       "\n",
       "[2 rows x 26 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fc_file = '../featureCounts/all_feature.txt'\n",
    "df = pd.read_csv(fc_file, header=1, sep='\\t')\n",
    "df_geneid = df.iloc[:, 0:1]\n",
    "# 1,2,3,4列是基因坐标，下游分析不需要，如有需要回来再找\n",
    "df_counts = df.iloc[:, 5:]\n",
    "df_merge = pd.concat([df_geneid, df_counts], axis=1)\n",
    "df_merge.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Length</th>\n",
       "      <th>CTCF_AID_auxin1day_rep1</th>\n",
       "      <th>CTCF_AID_auxin1day_rep2</th>\n",
       "      <th>CTCF_AID_auxin1day_rep3</th>\n",
       "      <th>CTCF_AID_auxin2days_rep1</th>\n",
       "      <th>CTCF_AID_auxin2days_rep2</th>\n",
       "      <th>CTCF_AID_auxin2days_rep3</th>\n",
       "      <th>CTCF_AID_auxin4days_rep1</th>\n",
       "      <th>CTCF_AID_auxin4days_rep2</th>\n",
       "      <th>CTCF_AID_auxin4days_rep3</th>\n",
       "      <th>...</th>\n",
       "      <th>CTCF_AID_washoff2days_rep3</th>\n",
       "      <th>WT_untagged_auxin2days_rep1</th>\n",
       "      <th>WT_untagged_auxin2days_rep2</th>\n",
       "      <th>WT_untagged_auxin2days_rep3</th>\n",
       "      <th>WT_untagged_auxin4days_rep1</th>\n",
       "      <th>WT_untagged_auxin4days_rep2</th>\n",
       "      <th>WT_untagged_auxin4days_rep3</th>\n",
       "      <th>WT_untagged_untreated_rep1</th>\n",
       "      <th>WT_untagged_untreated_rep2</th>\n",
       "      <th>WT_untagged_untreated_rep3</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Geneid</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSMUSG00000102693.1</th>\n",
       "      <td>1070</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSMUSG00000064842.1</th>\n",
       "      <td>110</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2 rows × 25 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      Length  CTCF_AID_auxin1day_rep1  \\\n",
       "Geneid                                                  \n",
       "ENSMUSG00000102693.1    1070                        0   \n",
       "ENSMUSG00000064842.1     110                        0   \n",
       "\n",
       "                      CTCF_AID_auxin1day_rep2  CTCF_AID_auxin1day_rep3  \\\n",
       "Geneid                                                                   \n",
       "ENSMUSG00000102693.1                        0                        0   \n",
       "ENSMUSG00000064842.1                        0                        0   \n",
       "\n",
       "                      CTCF_AID_auxin2days_rep1  CTCF_AID_auxin2days_rep2  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                         0                         0   \n",
       "ENSMUSG00000064842.1                         0                         0   \n",
       "\n",
       "                      CTCF_AID_auxin2days_rep3  CTCF_AID_auxin4days_rep1  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                         0                         0   \n",
       "ENSMUSG00000064842.1                         0                         0   \n",
       "\n",
       "                      CTCF_AID_auxin4days_rep2  CTCF_AID_auxin4days_rep3  ...  \\\n",
       "Geneid                                                                    ...   \n",
       "ENSMUSG00000102693.1                         0                         0  ...   \n",
       "ENSMUSG00000064842.1                         0                         0  ...   \n",
       "\n",
       "                      CTCF_AID_washoff2days_rep3  WT_untagged_auxin2days_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                           0                            0   \n",
       "ENSMUSG00000064842.1                           0                            0   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                            0   \n",
       "ENSMUSG00000064842.1                            0   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep3  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                            0   \n",
       "ENSMUSG00000064842.1                            0   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep1  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                            0   \n",
       "ENSMUSG00000064842.1                            0   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                            3   \n",
       "ENSMUSG00000064842.1                            0   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep3  WT_untagged_untreated_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                            0                           0   \n",
       "ENSMUSG00000064842.1                            0                           0   \n",
       "\n",
       "                      WT_untagged_untreated_rep2  WT_untagged_untreated_rep3  \n",
       "Geneid                                                                        \n",
       "ENSMUSG00000102693.1                           1                           0  \n",
       "ENSMUSG00000064842.1                           0                           0  \n",
       "\n",
       "[2 rows x 25 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# df = df.copy()\n",
    "df_merge.columns=ordered_bam_labels\n",
    "df_merge.set_index('Geneid', inplace=True)\n",
    "df_merge.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 12.5 ms, sys: 13.2 ms, total: 25.7 ms\n",
      "Wall time: 25.2 ms\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CTCF_AID_auxin1day_rep1</th>\n",
       "      <th>CTCF_AID_auxin1day_rep2</th>\n",
       "      <th>CTCF_AID_auxin1day_rep3</th>\n",
       "      <th>CTCF_AID_auxin2days_rep1</th>\n",
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       "      <th>CTCF_AID_auxin2days_rep3</th>\n",
       "      <th>CTCF_AID_auxin4days_rep1</th>\n",
       "      <th>CTCF_AID_auxin4days_rep2</th>\n",
       "      <th>CTCF_AID_auxin4days_rep3</th>\n",
       "      <th>CTCF_AID_untreated_rep1</th>\n",
       "      <th>...</th>\n",
       "      <th>CTCF_AID_washoff2days_rep3</th>\n",
       "      <th>WT_untagged_auxin2days_rep1</th>\n",
       "      <th>WT_untagged_auxin2days_rep2</th>\n",
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       "      <th>WT_untagged_auxin4days_rep1</th>\n",
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       "      <th>WT_untagged_untreated_rep3</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Geneid</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "</table>\n",
       "<p>2 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      CTCF_AID_auxin1day_rep1  CTCF_AID_auxin1day_rep2  \\\n",
       "Geneid                                                                   \n",
       "ENSMUSG00000102693.1                      0.0                      0.0   \n",
       "ENSMUSG00000064842.1                      0.0                      0.0   \n",
       "\n",
       "                      CTCF_AID_auxin1day_rep3  CTCF_AID_auxin2days_rep1  \\\n",
       "Geneid                                                                    \n",
       "ENSMUSG00000102693.1                      0.0                       0.0   \n",
       "ENSMUSG00000064842.1                      0.0                       0.0   \n",
       "\n",
       "                      CTCF_AID_auxin2days_rep2  CTCF_AID_auxin2days_rep3  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                       0.0                       0.0   \n",
       "ENSMUSG00000064842.1                       0.0                       0.0   \n",
       "\n",
       "                      CTCF_AID_auxin4days_rep1  CTCF_AID_auxin4days_rep2  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                       0.0                       0.0   \n",
       "ENSMUSG00000064842.1                       0.0                       0.0   \n",
       "\n",
       "                      CTCF_AID_auxin4days_rep3  CTCF_AID_untreated_rep1  ...  \\\n",
       "Geneid                                                                   ...   \n",
       "ENSMUSG00000102693.1                       0.0                      0.0  ...   \n",
       "ENSMUSG00000064842.1                       0.0                      0.0  ...   \n",
       "\n",
       "                      CTCF_AID_washoff2days_rep3  WT_untagged_auxin2days_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                         0.0                          0.0   \n",
       "ENSMUSG00000064842.1                         0.0                          0.0   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                          0.0   \n",
       "ENSMUSG00000064842.1                          0.0   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep3  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                          0.0   \n",
       "ENSMUSG00000064842.1                          0.0   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep1  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                          0.0   \n",
       "ENSMUSG00000064842.1                          0.0   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                      0.03584   \n",
       "ENSMUSG00000064842.1                      0.00000   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep3  WT_untagged_untreated_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                          0.0                         0.0   \n",
       "ENSMUSG00000064842.1                          0.0                         0.0   \n",
       "\n",
       "                      WT_untagged_untreated_rep2  WT_untagged_untreated_rep3  \n",
       "Geneid                                                                        \n",
       "ENSMUSG00000102693.1                    0.006517                         0.0  \n",
       "ENSMUSG00000064842.1                    0.000000                         0.0  \n",
       "\n",
       "[2 rows x 24 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "# now, normalize raw counts using RPKM method\n",
    "# gene length must be in bp\n",
    "nm = norm()\n",
    "nm.rpkm(df=df_merge, gl='Length')\n",
    "# get RPKM normalized dataframe\n",
    "df_rpkm = nm.rpkm_norm\n",
    "df_rpkm.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>CTCF_AID_auxin1day_rep1</th>\n",
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      ],
      "text/plain": [
       "                      CTCF_AID_auxin1day_rep1  CTCF_AID_auxin1day_rep2  \\\n",
       "Geneid                                                                   \n",
       "ENSMUSG00000102693.1                 0.000000                 0.000000   \n",
       "ENSMUSG00000064842.1                 0.000000                 0.000000   \n",
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       "ENSMUSG00000103377.1                 0.000000                 0.000000   \n",
       "...                                       ...                      ...   \n",
       "ENSMUSG00000064368.1               755.267832              1702.529809   \n",
       "ENSMUSG00000064369.1                 0.000000                 4.074751   \n",
       "ENSMUSG00000064370.1              1506.275169              2942.399026   \n",
       "ENSMUSG00000064371.1                 0.000000                 0.000000   \n",
       "ENSMUSG00000064372.1               134.823565               141.689734   \n",
       "\n",
       "                      CTCF_AID_auxin1day_rep3  CTCF_AID_auxin2days_rep1  \\\n",
       "Geneid                                                                    \n",
       "ENSMUSG00000102693.1                 0.000000                  0.000000   \n",
       "ENSMUSG00000064842.1                 0.000000                  0.000000   \n",
       "ENSMUSG00000051951.5                 0.070452                  0.241819   \n",
       "ENSMUSG00000102851.1                 0.000000                  0.000000   \n",
       "ENSMUSG00000103377.1                 0.000000                  0.000000   \n",
       "...                                       ...                       ...   \n",
       "ENSMUSG00000064368.1              1973.405991                922.388532   \n",
       "ENSMUSG00000064369.1                 6.857150                 12.458350   \n",
       "ENSMUSG00000064370.1              3328.838197               2152.151505   \n",
       "ENSMUSG00000064371.1                 0.653874                  0.000000   \n",
       "ENSMUSG00000064372.1               198.123887                 96.685028   \n",
       "\n",
       "                      CTCF_AID_auxin2days_rep2  CTCF_AID_auxin2days_rep3  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000064842.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000051951.5                  0.058030                  0.084357   \n",
       "ENSMUSG00000102851.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000103377.1                  0.011947                  0.008289   \n",
       "...                                        ...                       ...   \n",
       "ENSMUSG00000064368.1               1495.156984               3097.500576   \n",
       "ENSMUSG00000064369.1                  3.416734                  9.143608   \n",
       "ENSMUSG00000064370.1               3017.250477               3782.093815   \n",
       "ENSMUSG00000064371.1                  0.000000                  0.697522   \n",
       "ENSMUSG00000064372.1                149.294531                318.942099   \n",
       "\n",
       "                      CTCF_AID_auxin4days_rep1  CTCF_AID_auxin4days_rep2  \\\n",
       "Geneid                                                                     \n",
       "ENSMUSG00000102693.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000064842.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000051951.5                  0.147187                  0.103706   \n",
       "ENSMUSG00000102851.1                  0.000000                  0.000000   \n",
       "ENSMUSG00000103377.1                  0.000000                  0.011209   \n",
       "...                                        ...                       ...   \n",
       "ENSMUSG00000064368.1                931.365814               2435.724179   \n",
       "ENSMUSG00000064369.1                  0.590881                  7.327345   \n",
       "ENSMUSG00000064370.1               2435.521990               3557.034205   \n",
       "ENSMUSG00000064371.1                  0.000000                  0.943259   \n",
       "ENSMUSG00000064372.1                105.273912                176.861062   \n",
       "\n",
       "                      CTCF_AID_auxin4days_rep3  CTCF_AID_untreated_rep1  ...  \\\n",
       "Geneid                                                                   ...   \n",
       "ENSMUSG00000102693.1                  0.000000                 0.000000  ...   \n",
       "ENSMUSG00000064842.1                  0.000000                 0.000000  ...   \n",
       "ENSMUSG00000051951.5                  0.164153                 0.049543  ...   \n",
       "ENSMUSG00000102851.1                  0.000000                 0.000000  ...   \n",
       "ENSMUSG00000103377.1                  0.000000                 0.000000  ...   \n",
       "...                                        ...                      ...  ...   \n",
       "ENSMUSG00000064368.1               2778.132803               851.811883  ...   \n",
       "ENSMUSG00000064369.1                  6.372648                 5.625752  ...   \n",
       "ENSMUSG00000064370.1               4029.530651              1769.831836  ...   \n",
       "ENSMUSG00000064371.1                  0.492216                 0.000000  ...   \n",
       "ENSMUSG00000064372.1                307.798891                97.848905  ...   \n",
       "\n",
       "                      CTCF_AID_washoff2days_rep3  WT_untagged_auxin2days_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                    0.000000                     0.000000   \n",
       "ENSMUSG00000064842.1                    0.000000                     0.000000   \n",
       "ENSMUSG00000051951.5                    0.058405                     0.038374   \n",
       "ENSMUSG00000102851.1                    0.000000                     0.000000   \n",
       "ENSMUSG00000103377.1                    0.000000                     0.000000   \n",
       "...                                          ...                          ...   \n",
       "ENSMUSG00000064368.1                 2290.394707                  1739.779062   \n",
       "ENSMUSG00000064369.1                    5.613424                     6.231715   \n",
       "ENSMUSG00000064370.1                 3305.294760                  3151.394862   \n",
       "ENSMUSG00000064371.1                    0.468729                     0.337776   \n",
       "ENSMUSG00000064372.1                  196.397397                   131.056932   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                     0.000000   \n",
       "ENSMUSG00000064842.1                     0.000000   \n",
       "ENSMUSG00000051951.5                     0.007817   \n",
       "ENSMUSG00000102851.1                     0.000000   \n",
       "ENSMUSG00000103377.1                     0.000000   \n",
       "...                                           ...   \n",
       "ENSMUSG00000064368.1                 11683.613470   \n",
       "ENSMUSG00000064369.1                    57.994790   \n",
       "ENSMUSG00000064370.1                  4034.225435   \n",
       "ENSMUSG00000064371.1                     6.399212   \n",
       "ENSMUSG00000064372.1                   290.453116   \n",
       "\n",
       "                      WT_untagged_auxin2days_rep3  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                     0.000000   \n",
       "ENSMUSG00000064842.1                     0.000000   \n",
       "ENSMUSG00000051951.5                     0.065504   \n",
       "ENSMUSG00000102851.1                     0.000000   \n",
       "ENSMUSG00000103377.1                     0.000000   \n",
       "...                                           ...   \n",
       "ENSMUSG00000064368.1                  2337.361517   \n",
       "ENSMUSG00000064369.1                     9.466772   \n",
       "ENSMUSG00000064370.1                  3917.107880   \n",
       "ENSMUSG00000064371.1                     0.000000   \n",
       "ENSMUSG00000064372.1                   133.602377   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep1  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                     0.000000   \n",
       "ENSMUSG00000064842.1                     0.000000   \n",
       "ENSMUSG00000051951.5                     0.059003   \n",
       "ENSMUSG00000102851.1                     0.000000   \n",
       "ENSMUSG00000103377.1                     0.000000   \n",
       "...                                           ...   \n",
       "ENSMUSG00000064368.1                  1505.652361   \n",
       "ENSMUSG00000064369.1                     9.941071   \n",
       "ENSMUSG00000064370.1                  3185.233882   \n",
       "ENSMUSG00000064371.1                     0.082563   \n",
       "ENSMUSG00000064372.1                   161.328214   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep2  \\\n",
       "Geneid                                              \n",
       "ENSMUSG00000102693.1                     0.035840   \n",
       "ENSMUSG00000064842.1                     0.000000   \n",
       "ENSMUSG00000051951.5                     0.016781   \n",
       "ENSMUSG00000102851.1                     0.000000   \n",
       "ENSMUSG00000103377.1                     0.013604   \n",
       "...                                           ...   \n",
       "ENSMUSG00000064368.1                  3786.013820   \n",
       "ENSMUSG00000064369.1                    15.932350   \n",
       "ENSMUSG00000064370.1                  4212.646522   \n",
       "ENSMUSG00000064371.1                     0.190790   \n",
       "ENSMUSG00000064372.1                   176.671567   \n",
       "\n",
       "                      WT_untagged_auxin4days_rep3  WT_untagged_untreated_rep1  \\\n",
       "Geneid                                                                          \n",
       "ENSMUSG00000102693.1                     0.000000                    0.000000   \n",
       "ENSMUSG00000064842.1                     0.000000                    0.000000   \n",
       "ENSMUSG00000051951.5                     0.062350                    0.116738   \n",
       "ENSMUSG00000102851.1                     0.000000                    0.000000   \n",
       "ENSMUSG00000103377.1                     0.000000                    0.000000   \n",
       "...                                           ...                         ...   \n",
       "ENSMUSG00000064368.1                  2333.855717                 2106.911741   \n",
       "ENSMUSG00000064369.1                     8.259977                    9.737355   \n",
       "ENSMUSG00000064370.1                  4196.254620                 3574.652162   \n",
       "ENSMUSG00000064371.1                     0.000000                    0.000000   \n",
       "ENSMUSG00000064372.1                   165.026944                   99.493710   \n",
       "\n",
       "                      WT_untagged_untreated_rep2  WT_untagged_untreated_rep3  \n",
       "Geneid                                                                        \n",
       "ENSMUSG00000102693.1                    0.006517                    0.000000  \n",
       "ENSMUSG00000064842.1                    0.000000                    0.000000  \n",
       "ENSMUSG00000051951.5                    0.032041                    0.074641  \n",
       "ENSMUSG00000102851.1                    0.000000                    0.000000  \n",
       "ENSMUSG00000103377.1                    0.007421                    0.000000  \n",
       "...                                          ...                         ...  \n",
       "ENSMUSG00000064368.1                 2490.855007                 1727.682943  \n",
       "ENSMUSG00000064369.1                    9.601191                    7.107214  \n",
       "ENSMUSG00000064370.1                 3567.565205                 3747.222699  \n",
       "ENSMUSG00000064371.1                    0.208164                    0.318233  \n",
       "ENSMUSG00000064372.1                  134.786238                  129.839254  \n",
       "\n",
       "[55401 rows x 24 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_rpkm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# save rpkm\n",
    "df_rpkm.to_excel('../featureCounts/all_feature_rpkm.xlsx')\n",
    "# save raw_counts\n",
    "df_merge.to_excel('../featureCounts/all_feature_raw_counts.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "55401\n"
     ]
    }
   ],
   "source": [
    "# 按照 RPKM 每个 Gene 的均值大于 1 的条件过滤基因\n",
    "\n",
    "# 或者不进行过滤\n",
    "print(df_rpkm.shape[0])\n",
    "\n",
    "flt = df_rpkm.sum(axis=1) /df_rpkm.shape[1] >= 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Geneid</th>\n",
       "      <th>Length</th>\n",
       "      <th>CTCF_AID_auxin1day_rep1</th>\n",
       "      <th>CTCF_AID_auxin1day_rep2</th>\n",
       "      <th>CTCF_AID_auxin1day_rep3</th>\n",
       "      <th>CTCF_AID_auxin2days_rep1</th>\n",
       "      <th>CTCF_AID_auxin2days_rep2</th>\n",
       "      <th>CTCF_AID_auxin2days_rep3</th>\n",
       "      <th>CTCF_AID_auxin4days_rep1</th>\n",
       "      <th>CTCF_AID_auxin4days_rep2</th>\n",
       "      <th>...</th>\n",
       "      <th>CTCF_AID_washoff2days_rep3</th>\n",
       "      <th>WT_untagged_auxin2days_rep1</th>\n",
       "      <th>WT_untagged_auxin2days_rep2</th>\n",
       "      <th>WT_untagged_auxin2days_rep3</th>\n",
       "      <th>WT_untagged_auxin4days_rep1</th>\n",
       "      <th>WT_untagged_auxin4days_rep2</th>\n",
       "      <th>WT_untagged_auxin4days_rep3</th>\n",
       "      <th>WT_untagged_untreated_rep1</th>\n",
       "      <th>WT_untagged_untreated_rep2</th>\n",
       "      <th>WT_untagged_untreated_rep3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "      <td>6094</td>\n",
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       "      <td>49</td>\n",
       "      <td>48</td>\n",
       "      <td>21</td>\n",
       "      <td>44</td>\n",
       "      <td>22</td>\n",
       "      <td>40</td>\n",
       "      <td>...</td>\n",
       "      <td>34</td>\n",
       "      <td>31</td>\n",
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       "      <td>33</td>\n",
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       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>18</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55400</th>\n",
       "      <td>ENSMUSG00000064372.1</td>\n",
       "      <td>67</td>\n",
       "      <td>226</td>\n",
       "      <td>574</td>\n",
       "      <td>1515</td>\n",
       "      <td>211</td>\n",
       "      <td>594</td>\n",
       "      <td>1829</td>\n",
       "      <td>173</td>\n",
       "      <td>750</td>\n",
       "      <td>...</td>\n",
       "      <td>1257</td>\n",
       "      <td>1164</td>\n",
       "      <td>817</td>\n",
       "      <td>740</td>\n",
       "      <td>1954</td>\n",
       "      <td>926</td>\n",
       "      <td>582</td>\n",
       "      <td>506</td>\n",
       "      <td>1295</td>\n",
       "      <td>1224</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55401 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                     Geneid  Length  CTCF_AID_auxin1day_rep1  \\\n",
       "0      ENSMUSG00000102693.1    1070                        0   \n",
       "1      ENSMUSG00000064842.1     110                        0   \n",
       "2      ENSMUSG00000051951.5    6094                        2   \n",
       "3      ENSMUSG00000102851.1     480                        0   \n",
       "4      ENSMUSG00000103377.1    2819                        0   \n",
       "...                     ...     ...                      ...   \n",
       "55396  ENSMUSG00000064368.1     519                     9807   \n",
       "55397  ENSMUSG00000064369.1      69                        0   \n",
       "55398  ENSMUSG00000064370.1    1144                    43112   \n",
       "55399  ENSMUSG00000064371.1      67                        0   \n",
       "55400  ENSMUSG00000064372.1      67                      226   \n",
       "\n",
       "       CTCF_AID_auxin1day_rep2  CTCF_AID_auxin1day_rep3  \\\n",
       "0                            0                        0   \n",
       "1                            0                        0   \n",
       "2                           14                       49   \n",
       "3                            0                        0   \n",
       "4                            0                        0   \n",
       "...                        ...                      ...   \n",
       "55396                    53427                   116892   \n",
       "55397                       17                       54   \n",
       "55398                   203529                   434630   \n",
       "55399                        0                        5   \n",
       "55400                      574                     1515   \n",
       "\n",
       "       CTCF_AID_auxin2days_rep1  CTCF_AID_auxin2days_rep2  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                            48                        21   \n",
       "3                             0                         0   \n",
       "4                             0                         2   \n",
       "...                         ...                       ...   \n",
       "55396                     15593                     46081   \n",
       "55397                        28                        14   \n",
       "55398                     80195                    204977   \n",
       "55399                         0                         0   \n",
       "55400                       211                       594   \n",
       "\n",
       "       CTCF_AID_auxin2days_rep3  CTCF_AID_auxin4days_rep1  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                            44                        22   \n",
       "3                             0                         0   \n",
       "4                             2                         0   \n",
       "...                         ...                       ...   \n",
       "55396                    137596                     11856   \n",
       "55397                        54                         1   \n",
       "55398                    370327                     68339   \n",
       "55399                         4                         0   \n",
       "55400                      1829                       173   \n",
       "\n",
       "       CTCF_AID_auxin4days_rep2  ...  CTCF_AID_washoff2days_rep3  \\\n",
       "0                             0  ...                           0   \n",
       "1                             0  ...                           0   \n",
       "2                            40  ...                          34   \n",
       "3                             0  ...                           0   \n",
       "4                             2  ...                           0   \n",
       "...                         ...  ...                         ...   \n",
       "55396                     80011  ...                      113554   \n",
       "55397                        32  ...                          37   \n",
       "55398                    257554  ...                      361211   \n",
       "55399                         4  ...                           3   \n",
       "55400                       750  ...                        1257   \n",
       "\n",
       "       WT_untagged_auxin2days_rep1  WT_untagged_auxin2days_rep2  \\\n",
       "0                                0                            0   \n",
       "1                                0                            0   \n",
       "2                               31                            2   \n",
       "3                                0                            0   \n",
       "4                                0                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       119696                       254575   \n",
       "55397                           57                          168   \n",
       "55398                       477911                       193757   \n",
       "55399                            3                           18   \n",
       "55400                         1164                          817   \n",
       "\n",
       "       WT_untagged_auxin2days_rep3  WT_untagged_auxin4days_rep1  \\\n",
       "0                                0                            0   \n",
       "1                                0                            0   \n",
       "2                               33                           65   \n",
       "3                                0                            0   \n",
       "4                                0                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       100285                       141264   \n",
       "55397                           54                          124   \n",
       "55398                       370454                       658729   \n",
       "55399                            0                            1   \n",
       "55400                          740                         1954   \n",
       "\n",
       "       WT_untagged_auxin4days_rep2  WT_untagged_auxin4days_rep3  \\\n",
       "0                                3                            0   \n",
       "1                                0                            0   \n",
       "2                                8                           20   \n",
       "3                                0                            0   \n",
       "4                                3                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       153716                        63758   \n",
       "55397                           86                           30   \n",
       "55398                       377008                       252686   \n",
       "55399                            1                            0   \n",
       "55400                          926                          582   \n",
       "\n",
       "       WT_untagged_untreated_rep1  WT_untagged_untreated_rep2  \\\n",
       "0                               0                           1   \n",
       "1                               0                           0   \n",
       "2                              54                          28   \n",
       "3                               0                           0   \n",
       "4                               0                           3   \n",
       "...                           ...                         ...   \n",
       "55396                       83003                      185381   \n",
       "55397                          51                          95   \n",
       "55398                      310413                      585258   \n",
       "55399                           0                           2   \n",
       "55400                         506                        1295   \n",
       "\n",
       "       WT_untagged_untreated_rep3  \n",
       "0                               0  \n",
       "1                               0  \n",
       "2                              64  \n",
       "3                               0  \n",
       "4                               0  \n",
       "...                           ...  \n",
       "55396                      126163  \n",
       "55397                          69  \n",
       "55398                      603165  \n",
       "55399                           3  \n",
       "55400                        1224  \n",
       "\n",
       "[55401 rows x 26 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_flt_rawcounts = df_merge[flt].copy()\n",
    "df_flt_rawcounts.reset_index(inplace=True)\n",
    "df_flt_rawcounts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "df_flt_rawcounts.drop('Length', axis=1, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>Geneid</th>\n",
       "      <th>CTCF_AID_auxin1day_rep1</th>\n",
       "      <th>CTCF_AID_auxin1day_rep2</th>\n",
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       "      <td>22</td>\n",
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       "      <td>91</td>\n",
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       "      <td>34</td>\n",
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       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55401 rows × 25 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                     Geneid  CTCF_AID_auxin1day_rep1  CTCF_AID_auxin1day_rep2  \\\n",
       "0      ENSMUSG00000102693.1                        0                        0   \n",
       "1      ENSMUSG00000064842.1                        0                        0   \n",
       "2      ENSMUSG00000051951.5                        2                       14   \n",
       "3      ENSMUSG00000102851.1                        0                        0   \n",
       "4      ENSMUSG00000103377.1                        0                        0   \n",
       "...                     ...                      ...                      ...   \n",
       "55396  ENSMUSG00000064368.1                     9807                    53427   \n",
       "55397  ENSMUSG00000064369.1                        0                       17   \n",
       "55398  ENSMUSG00000064370.1                    43112                   203529   \n",
       "55399  ENSMUSG00000064371.1                        0                        0   \n",
       "55400  ENSMUSG00000064372.1                      226                      574   \n",
       "\n",
       "       CTCF_AID_auxin1day_rep3  CTCF_AID_auxin2days_rep1  \\\n",
       "0                            0                         0   \n",
       "1                            0                         0   \n",
       "2                           49                        48   \n",
       "3                            0                         0   \n",
       "4                            0                         0   \n",
       "...                        ...                       ...   \n",
       "55396                   116892                     15593   \n",
       "55397                       54                        28   \n",
       "55398                   434630                     80195   \n",
       "55399                        5                         0   \n",
       "55400                     1515                       211   \n",
       "\n",
       "       CTCF_AID_auxin2days_rep2  CTCF_AID_auxin2days_rep3  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                            21                        44   \n",
       "3                             0                         0   \n",
       "4                             2                         2   \n",
       "...                         ...                       ...   \n",
       "55396                     46081                    137596   \n",
       "55397                        14                        54   \n",
       "55398                    204977                    370327   \n",
       "55399                         0                         4   \n",
       "55400                       594                      1829   \n",
       "\n",
       "       CTCF_AID_auxin4days_rep1  CTCF_AID_auxin4days_rep2  \\\n",
       "0                             0                         0   \n",
       "1                             0                         0   \n",
       "2                            22                        40   \n",
       "3                             0                         0   \n",
       "4                             0                         2   \n",
       "...                         ...                       ...   \n",
       "55396                     11856                     80011   \n",
       "55397                         1                        32   \n",
       "55398                     68339                    257554   \n",
       "55399                         0                         4   \n",
       "55400                       173                       750   \n",
       "\n",
       "       CTCF_AID_auxin4days_rep3  ...  CTCF_AID_washoff2days_rep3  \\\n",
       "0                             0  ...                           0   \n",
       "1                             0  ...                           0   \n",
       "2                            91  ...                          34   \n",
       "3                             0  ...                           0   \n",
       "4                             0  ...                           0   \n",
       "...                         ...  ...                         ...   \n",
       "55396                    131163  ...                      113554   \n",
       "55397                        40  ...                          37   \n",
       "55398                    419345  ...                      361211   \n",
       "55399                         3  ...                           3   \n",
       "55400                      1876  ...                        1257   \n",
       "\n",
       "       WT_untagged_auxin2days_rep1  WT_untagged_auxin2days_rep2  \\\n",
       "0                                0                            0   \n",
       "1                                0                            0   \n",
       "2                               31                            2   \n",
       "3                                0                            0   \n",
       "4                                0                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       119696                       254575   \n",
       "55397                           57                          168   \n",
       "55398                       477911                       193757   \n",
       "55399                            3                           18   \n",
       "55400                         1164                          817   \n",
       "\n",
       "       WT_untagged_auxin2days_rep3  WT_untagged_auxin4days_rep1  \\\n",
       "0                                0                            0   \n",
       "1                                0                            0   \n",
       "2                               33                           65   \n",
       "3                                0                            0   \n",
       "4                                0                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       100285                       141264   \n",
       "55397                           54                          124   \n",
       "55398                       370454                       658729   \n",
       "55399                            0                            1   \n",
       "55400                          740                         1954   \n",
       "\n",
       "       WT_untagged_auxin4days_rep2  WT_untagged_auxin4days_rep3  \\\n",
       "0                                3                            0   \n",
       "1                                0                            0   \n",
       "2                                8                           20   \n",
       "3                                0                            0   \n",
       "4                                3                            0   \n",
       "...                            ...                          ...   \n",
       "55396                       153716                        63758   \n",
       "55397                           86                           30   \n",
       "55398                       377008                       252686   \n",
       "55399                            1                            0   \n",
       "55400                          926                          582   \n",
       "\n",
       "       WT_untagged_untreated_rep1  WT_untagged_untreated_rep2  \\\n",
       "0                               0                           1   \n",
       "1                               0                           0   \n",
       "2                              54                          28   \n",
       "3                               0                           0   \n",
       "4                               0                           3   \n",
       "...                           ...                         ...   \n",
       "55396                       83003                      185381   \n",
       "55397                          51                          95   \n",
       "55398                      310413                      585258   \n",
       "55399                           0                           2   \n",
       "55400                         506                        1295   \n",
       "\n",
       "       WT_untagged_untreated_rep3  \n",
       "0                               0  \n",
       "1                               0  \n",
       "2                              64  \n",
       "3                               0  \n",
       "4                               0  \n",
       "...                           ...  \n",
       "55396                      126163  \n",
       "55397                          69  \n",
       "55398                      603165  \n",
       "55399                           3  \n",
       "55400                        1224  \n",
       "\n",
       "[55401 rows x 25 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_flt_rawcounts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_flt_rawcounts.Geneid.duplicated().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# 过滤后的raw counts进入DESeq2处理\n",
    "df_flt_rawcounts.to_csv(fc_file.replace('.txt', '_fix_feed_to_deseq2.csv'), index=None, sep=',')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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