rNMP_match_analysis

Check whether incorporated rNMPs in DNA match reference genome Table of Contents

• Installation
  • Getting the code
  • Creating the enviroment with required dependencies
• Running Mismatch Removal
  • Configure run
  • Filtration
• Output

Installation

Getting the code

git clone https://github.com/DKundnani/rNMP_match_analysis.git 

Creating the enviroment with required dependencies

conda env create --file rNMP_match_analysis/mm_removal.yml

Running Mismatch Removal

Configure run

vim MMremoval_configure_run.sh
#Change the variables for you run as per mentions in the bash configure file

Filtration

bash MMremoval_configure_run.sh

Output

• From Mismatch Removal
  • Files with prefix 'MManalysis_' : chr start stop upstream+rNMP(sequencing data) upstream+rNMP(reference genome) strand (6 columns bed files)
  • Files with prefix 'poly_' : chr start stop upstream+rNMP(sequencing data) upstream+rNMP(reference genome) strand rNMP(sequencing data) rNMP(reference genome) (8 columns bed files)
  • files with prefix 'matches_' : Files with prefix 'poly_' filtered for matched column 7 & column 8
  • Files with suffix 'final.bed' : Files filtered for matched polyN upto user specified bases upstream of rNMP location
  • chrM_mismatch_percentage.txt & chrM_mismatch_percentage.txt: Difference between the percetage of rNMP bases between the bed file provided and final bed in mitochondria and nucleus