QC_mapping

Quality Control (QC) Analysis - Minimap2

Step 1:

Execute Script qc.sh

The qc.sh script performs the following operations:

• For each BAM file sorted in the directory :
  • Extracts the sample name from the file name.
  • Counts mapped and unmapped reads using Samtools ( on: /local/env/envsamtools-1.15.sh ) .
  • Saves results to a CSV file [count_output_dna.csv] (count_output_dna.csv) in the following path /groups/dog/stage/rahma/results/minimap2/analysis/QC/count_output_dna.csv

Step 2: Bar Plot generation

Run the script

Rscript qc_mapping.R

You will obtain this plot qc_mappng.pdf