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Results is a directory containing pre-made, well, results. The two BAM files are our test datasets, and they are a sub-sample of reads from only chr19. The ripseeker.cmds and ripseeker_script.R files are both commands files, which we will examine later. Before that, we need to make some adjustments so we can install some new libraries. First, execute these commands:
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cd $SCRATCH/ripseq_exercises/CLIP
cp /scratch/02423/nsabell/RIPSeeker_1.4.0.tar.gz .
cp /scratch/02423/nsabell/ripseeker_script.R .
mkdir lib
chmod 777 lib |
RIPSeeker
RIPSeeker is a Bioconductor R package, and we are going to run the job using the "Rscript" utility using the script and commands file that exist in the directory you just staged. Even on TINY files like the ones we are using, it will take a while to run, so we're going to kick it off now, and then look at what we're doing while it's processing.
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