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| Code Block |
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$BI/bin/launcher_creator.py -n ripseeker -t 01:00:00 -j ripseeker.cmds -q development -a CCBB
qsub ripseeker.sge |
The output should deposit several two files in your current directory, which includes the following:
| Code Block |
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...
RIPregions.gff3
seekOutput.RData |
The important file is RIPregions.gff3, which is a coordinate file of the regions predicted to be enriched in the IP. Because of the extremely slimmed-down dataset we used, there is only one peak, but this pipeline (with more reads that are actually real) would produce a file that is more interesting.
Alternatives
We could have added these lines to the ripseeker_script.R file:
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