Short read mapping pipeline pig
Jump to navigation
Jump to search
The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed
Prerequisites
Basic execution
Automated runfile creation
python3 ABGC_mapping_v2.py -i LW22F08 -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 10
IDS=`cat list.txt`
(testenv)[megen002@nfs01 NGStools]$ for ID in $IDS; do python3 ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 16; done