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cisMultiDeep: Identifying Cell Type-Specific Cis-Regulatory Regions by Automatically-Tuned Deep Neural Network and SHAP

alt text

Introduction

This repository presents the workflow to identify functional enhancers for each annotated cell type from a diverse collection of multi-omics profiles. The cell type is determined by expression of a specific set of genes that are governed by cis-regulatory elements in non-coding genomic regions. Recent studies have demonstrated that the cell type-specific CREs are not fully conserved (Villar et al., 2015), whereas the expression patterns of the cell type-specific genes are evolutionarily conserved (Shay et al., 2012). Here, we aim to identify the set of both ‘conserved’ and ‘non-conserved’ cell type-specific CREs that controls the expression of ‘conserved’ cell type-specific genes. cisMultiDeep employs automatically-tuned deep learning with SHAP feature importance assessment in cross-species single-cell multiomics data.

Environment

python = 3.10.2
R = 4.0.6

Requirement

Python libraries

git clone https://github.com/ytanaka-bio/BICCN_Challenge_2023
cd BICCN_Challenge_2023
pip install -r requirements.txt --user

R libraries

Other softwares

Methods

1. Download and Preprocess datasets

1.1. Download cross-species' multi-omics datasets that were provided from BICCN committee using AWS CLI as follow:

aws s3 sync s3://biccn-challenge . --no-sign-request

1.2. Add "chr" into Macaque bedpe files:

mkdir snm3C/Macaque2
mkdir snm3C/Macaque2/HiC_Loops
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Astro.loop.bedpe > snm3C/Macaque2/HiC_Loops/Astro.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/CLA.loop.bedpe > snm3C/Macaque2/HiC_Loops/CLA.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L23.loop.bedpe > snm3C/Macaque2/HiC_Loops/L23.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L4.loop.bedpe > snm3C/Macaque2/HiC_Loops/L4.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L5-ET.loop.bedpe > snm3C/Macaque2/HiC_Loops/L5-ET.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L5-IT.loop.bedpe > snm3C/Macaque2/HiC_Loops/L5-IT.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L6b.loop.bedpe > snm3C/Macaque2/HiC_Loops/L6b.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L6-CT.loop.bedpe > snm3C/Macaque2/HiC_Loops/L6-CT.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/L6-IT.loop.bedpe > snm3C/Macaque2/HiC_Loops/L6-IT.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Lamp5.loop.bedpe > snm3C/Macaque2/HiC_Loops/Lamp5.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/MG.loop.bedpe > snm3C/Macaque2/HiC_Loops/MG.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/NP.loop.bedpe > snm3C/Macaque2/HiC_Loops/NP.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/ODC.loop.bedpe > snm3C/Macaque2/HiC_Loops/ODC.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/OPC.loop.bedpe > snm3C/Macaque2/HiC_Loops/OPC.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Pvalb-BC.loop.bedpe > snm3C/Macaque2/HiC_Loops/Pvalb-BC.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Pvalb-ChC.loop.bedpe > snm3C/Macaque2/HiC_Loops/Pvalb-ChC.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Sncg.loop.bedpe > snm3C/Macaque2/HiC_Loops/Sncg.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Sst.loop.bedpe > snm3C/Macaque2/HiC_Loops/Sst.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Vip.loop.bedpe > snm3C/Macaque2/HiC_Loops/Vip.loop.bedpe 
awk 'OFS="\t" {$1="chr"$1; $4="chr"$4; print}' snm3C/Macaque/HiC_Loops/Vsc.loop.bedpe > snm3C/Macaque2/HiC_Loops/Vsc.loop.bedpe

1.3. Download gene coordinate GTF files as follow:

#Human
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.annotation.gtf.gz
zcat gencode.v33.annotation.gtf.gz | grep gene_name | awk 'OFS="\t" {if ($3=="gene") {print $1,$4-1,$5,$14,$7}}' | tr -d '";' | sort -k1,1 -k2,2n -k3,3n > Human_gene.bed
mv gencode.v33.annotation.gtf.gz Human_gene.gtf.gz

#Macaque
wget https://ftp.ensembl.org/pub/release-110/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.110.gtf.gz
zcat Macaca_mulatta.Mmul_10.110.gtf.gz | sed -E 's/^(\w+)/chr\1/g' > Macaque_gene.gtf
rm Macaca_mulatta.Mmul_10.110.gtf.gz
grep gene_name Macaque_gene.gtf | awk 'OFS="\t" {if ($3=="gene") {print $1,$4-1,$5,$14,$7}}' | tr -d '";' | sort -k1,1 -k2,2n -k3,3n > Macaque_gene.bed
gzip Macaque_gene.gtf 

#Marmoset
wget https://hgdownload.soe.ucsc.edu/goldenPath/calJac4/bigZips/genes/ncbiRefSeq.gtf.gz
zcat ncbiRefSeq.gtf.gz | grep gene_name | awk 'OFS="\t" {if ($3=="transcript") {print $1,$4-1,$5,$14,$7}}' | tr -d '";' | sort -k1,1 -k2,2n -k3,3n > Marmoset_gene.bed
mv ncbiRefSeq.gtf.gz Marmoset_gene.gtf.gz

#Mouse
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/gencode.vM22.annotation.gtf.gz
zcat gencode.vM22.annotation.gtf.gz | grep gene_name | awk 'OFS="\t" {if ($3=="gene") {print $1,$4-1,$5,$14,$7}}' | tr -d '";' | sort -k1,1 -k2,2n -k3,3n > Mouse_gene.bed
mv gencode.vM22.annotation.gtf.gz Mouse_gene.gtf.gz

1.4. Remove duplicated genes from BED file:

R CMD BATCH remove_duplicate_gene_bed.R

1.5. Obtain orthologous gene list from Biomart as follow:

  • Choose "Ensembl Gene 10" and "Human genes (GRCh39.p14)"
  • In Attributes section, choose "Homologues (Max select 6 orthologues)"
  • In GENE tab, choose "Gene stable ID" and "Gene name"
  • In ORTHOLOGUES [K-O] tab, choose "Macaque gene table ID", "Macaque gene name", "Mouse gene stable ID", and "Mouse gene name"
  • In ORTHOLOGUES [U-Z] tab, choose "White-tufted-ear marmoset gene stable ID" and "White-tufted-ear marmoset gene name"
  • Click "Result"
  • Choose "compressed file (.gz)" in export all results, and click "GO"

2. Calculate the cell type specificity score for each gene and peak

2.1. Calculate the cell type specificity score for each gene from transcriptome (RNA):

python identify_celltype_gene.py

2.2. Calculate the cell type specificity score for each gene from methylome (mCG, mCH):

python identify_celltype_methyl.py

2.3. Calculate the cell type specificity score for each peak from chromatin accessibility profiles (ATAC):

python identify_celltype_peak.py

3. Identification of conserved peaks across species

3.1. Download LiftOver UCSC Chain files:

wget https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToHg38.over.chain.gz       #Mouse vs Human
wget https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToRheMac10.over.chain.gz   #Mouse vs Macaque
wget https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToCalJac4.over.chain.gz    #Mouse vs Marmoset

3.2. Generate BED format files of ATAC peaks:

R CMD BATCH get_atac_bed.R

3.3. Run LiftOver command to identify orthologous regions of Mouse ATAC peaks in other species' genomes:

liftOver Mouse_atac.bed mm10ToHg38.over.chain.gz Mouse_atac_Human.bed Mouse_atac_Human_unmapped.bed
liftOver Mouse_atac.bed mm10ToRheMac10.over.chain.gz Mouse_atac_Macaque.bed Mouse_atac_Macaque_unmapped.bed
liftOver Mouse_atac.bed mm10ToCalJac4.over.chain.gz Mouse_atac_Marmoset.bed Mouse_atac_Marmoset_unmapped.bed

3.4. Run intersect command of BEDTools to identify ATAC peaks in each species corresponding to Mouse ATAC peaks:

bedtools intersect -a Mouse_atac_Human.bed -b Human_atac.bed -wa -wb -f 0.5  > Mouse_atac_Human_overlap.bed
bedtools intersect -a Mouse_atac_Macaque.bed -b Macaque_atac.bed -wa -wb -f 0.5  > Mouse_atac_Macaque_overlap.bed
bedtools intersect -a Mouse_atac_Marmoset.bed -b Marmoset_atac.bed -wa -wb -f 0.5  > Mouse_atac_Marmoset_overlap.bed

4. Get the list and dataset of orthologous genes and peaks for Deep Learning

4.1. Get conserved gene/peak list using a R script get_cons_data.R:

R CMD BATCH get_cons_data.R

4.2. Prepare input and output dataset for Deep Learning (Here, we focus on top 1000/10000 differential genes/peaks in each cell type):

#RNA, mCG, mCH
python prepare_cons_dataset.py -f 10XMultiome/Mouse/Mouse_rna.h5ad 10XMultiome/Human/Human_rna.h5ad 10XMultiome/Macaque/Macaque_rna.h5ad 10XMultiome/Marmoset/Marmoset_rna.h5ad -d all_rna_dif_cons.csv -a subclass_Bakken_2022 -r cons_rna_list.csv -o rna_1000 -g 1000
python prepare_cons_dataset.py -f snm3C/Mouse/Mouse_mCG_gene_fractions.h5ad snm3C/Human/Human_mCG_gene_fractions.h5ad snm3C/Macaque/Macaque_mCG_gene_fractions.h5ad snm3C/Marmoset/Marmoset_mCG_gene_fractions.h5ad -d all_mCG_dif_cons.csv -a subclass_Bakken_2022 -r cons_mCG_list.csv -o mCG_1000 -g 1000 -n False
python prepare_cons_dataset.py -f snm3C/Mouse/Mouse_mCH_gene_fractions.h5ad snm3C/Human/Human_mCH_gene_fractions.h5ad snm3C/Macaque/Maacque_mCH_gene_fractions.h5ad snm3C/Marmoset/Marmoset_mCH_gene_fractions.h5ad -d all_mCH_dif_cons.csv -a subclass_Bakken_2022 -r cons_mCH_list.csv -o mCH_1000 -g 1000 -n False

#ATAC
python prepare_dataset.py -f 10XMultiome/Mouse/Mouse_atac.h5ad -d Mouse_atac_dif_selected.csv -a subclass_Bakken_2022 -o Mouse_atac_10000 -g 10000
python prepare_dataset.py -f 10XMultiome/Human/Human_atac.h5ad -d Human_atac_dif_selected.csv -a subclass_Bakken_2022 -o Human_atac_10000 -g 10000
python prepare_dataset.py -f 10XMultiome/Macaque/Macaque_atac.h5ad -d Macaque_atac_dif_selected.csv -a subclass_Bakken_2022 -o Macaque_atac_10000 -g 10000
python prepare_dataset.py -f 10XMultiome/Marmoset/Marmoset_atac.h5ad -d Marmoset_atac_dif_selected.csv -a subclass_Bakken_2022 -o Marmoset_atac_10000 -g 10000

5. Deep learning and SHAP value calculation

5.1. Train Deep learning model and calculate the contribution (SHAP value) of each gene/peak to the segregation of cell types:

#RNA, mCG, mCH of conserved genes
python DeepSHAP_sparse.py -i rna_1000 -p rna_1000_output.csv -o rna_1000_deep_DR -t 12
python DeepSHAP_sparse.py -i mCG_1000 -p mCG_1000_output.csv -o mCG_1000_deep_DR -t 12
python DeepSHAP_sparse.py -i mCH_1000 -p mCH_1000_output.csv -o mCH_1000_deep_DR -t 12

#Mouse ATAC peaks
python DeepSHAP_sparse.py -i Mouse_atac_10000 -p Mouse_atac_10000_output.csv -o Mouse_atac_10000_deep_DR -t 12
python DeepSHAP_sparse.py -i Human_atac_10000 -p Human_atac_10000_output.csv -o Human_atac_10000_deep_DR -t 12
python DeepSHAP_sparse.py -i Macaque_atac_10000 -p Macaque_atac_10000_output.csv -o Macaque_atac_10000_deep_DR -t 12
python DeepSHAP_sparse.py -i Marmoset_atac_10000 -p Marmoset_atac_10000_output.csv -o Marmoset_atac_10000_deep_DR -t 12

6. Identify peaks and genes within the same HiC loop

6.1. Prepare gene and peak BED file for differential genes/peaks:

R CMD BATCH prepare_bed.R

6.2. Identify genes and peaks within each HiC loop:

mkdir inLoop

#Human ATAC
bedtools pairtobed -a snm3C/Human/HiC_Loops/Astro.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Astro.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/CLA.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_CLA.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L23.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L23.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-ET.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L5-ET.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-IT.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L5-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/NP.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_NP.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-CT.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L6-CT.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-IT.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L6-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6b.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_L6b.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Lamp5.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Lamp5.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/MG.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_MG.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/ODC.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_ODC.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/OPC.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_OPC.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Pvalb-BC.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Pvalb-BC.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sncg.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Sncg.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sst.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Sst.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vip.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Vip.loop_atac.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vsc.loop.bedpe -b Human_atac_10000.bed > inLoop/Human_Vsc.loop_atac.txt

#Human RNA
bedtools pairtobed -a snm3C/Human/HiC_Loops/Astro.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Astro.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/CLA.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_CLA.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L23.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L23.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-ET.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L5-ET.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-IT.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L5-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/NP.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_NP.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-CT.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L6-CT.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-IT.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L6-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6b.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_L6b.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Lamp5.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Lamp5.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/MG.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_MG.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/ODC.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_ODC.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/OPC.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_OPC.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Pvalb-BC.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Pvalb-BC.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sncg.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Sncg.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sst.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Sst.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vip.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Vip.loop_rna.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vsc.loop.bedpe -b Human_rna_1000.bed > inLoop/Human_Vsc.loop_rna.txt

#Human mCG
bedtools pairtobed -a snm3C/Human/HiC_Loops/Astro.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Astro.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/CLA.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_CLA.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L23.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L23.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-ET.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L5-ET.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-IT.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L5-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/NP.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_NP.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-CT.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L6-CT.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-IT.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L6-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6b.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_L6b.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Lamp5.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Lamp5.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/MG.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_MG.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/ODC.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_ODC.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/OPC.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_OPC.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Pvalb-BC.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Pvalb-BC.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sncg.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Sncg.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sst.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Sst.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vip.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Vip.loop_mCG.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vsc.loop.bedpe -b Human_mCG_1000.bed > inLoop/Human_Vsc.loop_mCG.txt

#Human mCH
bedtools pairtobed -a snm3C/Human/HiC_Loops/Astro.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Astro.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/CLA.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_CLA.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L23.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L23.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-ET.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L5-ET.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L5-IT.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L5-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/NP.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_NP.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-CT.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L6-CT.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6-IT.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L6-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/L6b.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_L6b.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Lamp5.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Lamp5.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/MG.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_MG.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/ODC.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_ODC.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/OPC.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_OPC.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Pvalb-BC.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Pvalb-BC.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sncg.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Sncg.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Sst.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Sst.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vip.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Vip.loop_mCH.txt
bedtools pairtobed -a snm3C/Human/HiC_Loops/Vsc.loop.bedpe -b Human_mCH_1000.bed > inLoop/Human_Vsc.loop_mCH.txt

#Macaque ATAC
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Astro.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Astro.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/CLA.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_CLA.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L23.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L23.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-ET.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L5-ET.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-IT.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L5-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/NP.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_NP.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-CT.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L6-CT.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-IT.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L6-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6b.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_L6b.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Lamp5.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Lamp5.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/MG.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_MG.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/ODC.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_ODC.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/OPC.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_OPC.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Pvalb-BC.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Pvalb-BC.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sncg.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Sncg.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sst.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Sst.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vip.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Vip.loop_atac.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vsc.loop.bedpe -b Macaque_atac_10000.bed > inLoop/Macaque_Vsc.loop_atac.txt

#Macaque RNA
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Astro.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Astro.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/CLA.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_CLA.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L23.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L23.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-ET.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L5-ET.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-IT.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L5-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/NP.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_NP.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-CT.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L6-CT.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-IT.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L6-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6b.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_L6b.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Lamp5.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Lamp5.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/MG.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_MG.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/ODC.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_ODC.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/OPC.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_OPC.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Pvalb-BC.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Pvalb-BC.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sncg.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Sncg.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sst.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Sst.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vip.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Vip.loop_rna.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vsc.loop.bedpe -b Macaque_rna_1000.bed > inLoop/Macaque_Vsc.loop_rna.txt

#Macaque mCG
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Astro.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Astro.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/CLA.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_CLA.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L23.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L23.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-ET.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L5-ET.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-IT.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L5-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/NP.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_NP.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-CT.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L6-CT.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-IT.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L6-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6b.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_L6b.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Lamp5.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Lamp5.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/MG.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_MG.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/ODC.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_ODC.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/OPC.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_OPC.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Pvalb-BC.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Pvalb-BC.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sncg.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Sncg.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sst.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Sst.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vip.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Vip.loop_mCG.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vsc.loop.bedpe -b Macaque_mCG_1000.bed > inLoop/Macaque_Vsc.loop_mCG.txt

#Macaque mCH
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Astro.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Astro.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/CLA.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_CLA.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L23.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L23.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-ET.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L5-ET.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L5-IT.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L5-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/NP.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_NP.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-CT.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L6-CT.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6-IT.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L6-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/L6b.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_L6b.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Lamp5.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Lamp5.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/MG.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_MG.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/ODC.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_ODC.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/OPC.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_OPC.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Pvalb-BC.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Pvalb-BC.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sncg.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Sncg.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Sst.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Sst.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vip.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Vip.loop_mCH.txt
bedtools pairtobed -a snm3C/Macaque2/HiC_Loops/Vsc.loop.bedpe -b Macaque_mCH_1000.bed > inLoop/Macaque_Vsc.loop_mCH.txt

#Marmoset ATAC
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Astro.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Astro.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/CLA.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_CLA.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L23.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L23.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-ET.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L5-ET.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-IT.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L5-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/NP.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_NP.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-CT.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L6-CT.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-IT.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L6-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6b.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_L6b.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Lamp5.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Lamp5.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/MG.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_MG.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/ODC.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_ODC.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/OPC.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_OPC.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Pvalb-BC.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Pvalb-BC.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sncg.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Sncg.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sst.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Sst.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vip.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Vip.loop_atac.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vsc.loop.bedpe -b Marmoset_atac_10000.bed > inLoop/Marmoset_Vsc.loop_atac.txt

#Marmoset RNA
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Astro.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Astro.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/CLA.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_CLA.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L23.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L23.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-ET.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L5-ET.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-IT.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L5-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/NP.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_NP.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-CT.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L6-CT.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-IT.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L6-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6b.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_L6b.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Lamp5.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Lamp5.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/MG.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_MG.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/ODC.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_ODC.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/OPC.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_OPC.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Pvalb-BC.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Pvalb-BC.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sncg.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Sncg.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sst.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Sst.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vip.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Vip.loop_rna.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vsc.loop.bedpe -b Marmoset_rna_1000.bed > inLoop/Marmoset_Vsc.loop_rna.txt

#Marmoset mCG
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Astro.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Astro.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/CLA.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_CLA.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L23.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L23.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-ET.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L5-ET.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-IT.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L5-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/NP.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_NP.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-CT.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L6-CT.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-IT.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L6-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6b.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_L6b.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Lamp5.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Lamp5.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/MG.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_MG.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/ODC.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_ODC.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/OPC.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_OPC.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Pvalb-BC.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Pvalb-BC.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sncg.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Sncg.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sst.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Sst.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vip.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Vip.loop_mCG.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vsc.loop.bedpe -b Marmoset_mCG_1000.bed > inLoop/Marmoset_Vsc.loop_mCG.txt

#Marmoset mCH
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Astro.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Astro.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/CLA.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_CLA.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L23.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L23.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-ET.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L5-ET.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L5-IT.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L5-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/NP.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_NP.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-CT.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L6-CT.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6-IT.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L6-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/L6b.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_L6b.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Lamp5.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Lamp5.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/MG.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_MG.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/ODC.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_ODC.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/OPC.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_OPC.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Pvalb-BC.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Pvalb-BC.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sncg.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Sncg.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Sst.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Sst.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vip.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Vip.loop_mCH.txt
bedtools pairtobed -a snm3C/Marmoset/HiC_Loops/Vsc.loop.bedpe -b Marmoset_mCH_1000.bed > inLoop/Marmoset_Vsc.loop_mCH.txt

#Mouse ATAC
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Astro.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Astro.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/CLA.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_CLA.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L23.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L23.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-ET.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L5-ET.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-IT.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L5-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/NP.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_NP.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-CT.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L6-CT.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-IT.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L6-IT.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6b.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_L6b.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Lamp5.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Lamp5.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/MG.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_MG.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/ODC.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_ODC.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/OPC.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_OPC.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Pvalb-BC.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Pvalb-BC.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sncg.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Sncg.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sst.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Sst.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vip.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Vip.loop_atac.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vsc.loop.bedpe -b Mouse_atac_10000.bed > inLoop/Mouse_Vsc.loop_atac.txt

#Mouse RNA
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Astro.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Astro.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/CLA.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_CLA.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L23.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L23.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-ET.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L5-ET.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-IT.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L5-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/NP.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_NP.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-CT.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L6-CT.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-IT.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L6-IT.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6b.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_L6b.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Lamp5.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Lamp5.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/MG.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_MG.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/ODC.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_ODC.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/OPC.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_OPC.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Pvalb-BC.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Pvalb-BC.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sncg.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Sncg.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sst.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Sst.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vip.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Vip.loop_rna.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vsc.loop.bedpe -b Mouse_rna_1000.bed > inLoop/Mouse_Vsc.loop_rna.txt

#Mouse mCG
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Astro.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Astro.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/CLA.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_CLA.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L23.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L23.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-ET.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L5-ET.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-IT.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L5-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/NP.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_NP.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-CT.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L6-CT.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-IT.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L6-IT.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6b.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_L6b.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Lamp5.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Lamp5.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/MG.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_MG.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/ODC.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_ODC.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/OPC.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_OPC.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Pvalb-BC.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Pvalb-BC.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sncg.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Sncg.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sst.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Sst.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vip.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Vip.loop_mCG.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vsc.loop.bedpe -b Mouse_mCG_1000.bed > inLoop/Mouse_Vsc.loop_mCG.txt

#Mouse mCH
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Astro.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Astro.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/CLA.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_CLA.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L23.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L23.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-ET.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L5-ET.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L5-IT.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L5-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/NP.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_NP.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-CT.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L6-CT.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6-IT.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L6-IT.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/L6b.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_L6b.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Lamp5.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Lamp5.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/MG.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_MG.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/ODC.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_ODC.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/OPC.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_OPC.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Pvalb-BC.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Pvalb-BC.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sncg.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Sncg.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Sst.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Sst.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vip.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Vip.loop_mCH.txt
bedtools pairtobed -a snm3C/Mouse/HiC_Loops/Vsc.loop.bedpe -b Mouse_mCH_1000.bed > inLoop/Mouse_Vsc.loop_mCH.txt

6.3. Calculate the sum of SHAP values of the connected genes by HiC loops.

R CMD BATCH all_sum_SHAP.R

References

BICCN Challenge