Short read mapping pipeline pig: Difference between revisions
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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` | IDS=`cat list.txt` | ||
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(testenv)[megen002@nfs01 NGStools]$ for ID in $IDS; do python3 ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 16; done | (testenv)[megen002@nfs01 NGStools]$ for ID in $IDS; do python3 ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 16; done | ||
== Output files == | |||
== See also == | |||
== External links == | |||
Revision as of 19:48, 27 December 2013
The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed
Prerequisites
Basic execution
Automated runfile creation
python3 ABGC_mapping_v2.py -i LW22F08 -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 10
IDS=`cat list.txt`
(testenv)[megen002@nfs01 NGStools]$ 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