1000Bulls mapping pipeline at ABGC: Difference between revisions
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(Created page with " <source lang='bash'> for i in `seq 1 15`; do echo $i; python3 ABGC_mapping_v2.py -i BOV-WUR-$i -a /srv/mds01/shared/Bulls1000/F12FPCEUHK0755_alq121122/cleandata/ -r /srv/mds01...") |
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for i in `seq 1 15`; do echo $i; python3 ABGC_mapping_v2.py -i BOV-WUR-$i -a /srv/mds01/shared/Bulls1000/F12FPCEUHK0755_alq121122/cleandata/ -r /srv/mds01/shared/Bulls1000/UMD31/umd_3_1.fa -t 12 -s cow -m bwa-aln -b 5.9 -o; done | for i in `seq 1 15`; do echo $i; python3 ABGC_mapping_v2.py -i BOV-WUR-$i -a /srv/mds01/shared/Bulls1000/F12FPCEUHK0755_alq121122/cleandata/ -r /srv/mds01/shared/Bulls1000/UMD31/umd_3_1.fa -t 12 -s cow -m bwa-aln -b 5.9 -o; done | ||
</source> | </source> | ||
* [https://github.com/hjmegens/NGStools/blob/master/ABGC_mapping_v2.py | * [https://github.com/hjmegens/NGStools/blob/master/ABGC_mapping_v2.py The Python3-based masterscript] | ||
* [https://github.com/hjmegens/NGStools/blob/master/runBOV-WUR-4.sh Example of a runfile created by the master script] | * [https://github.com/hjmegens/NGStools/blob/master/runBOV-WUR-4.sh Example of a runfile created by the master script] | ||
Revision as of 22:11, 26 November 2013
<source lang='bash'>
for i in `seq 1 15`; do echo $i; python3 ABGC_mapping_v2.py -i BOV-WUR-$i -a /srv/mds01/shared/Bulls1000/F12FPCEUHK0755_alq121122/cleandata/ -r /srv/mds01/shared/Bulls1000/UMD31/umd_3_1.fa -t 12 -s cow -m bwa-aln -b 5.9 -o; done </source>