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These are 101-base reads. wc -c counts the "invisible" newline character, so subtract 1 from the character count it returns for a line. Here's a way to strip the trailing newline characters from the quality scores string before calling wc -c to count the characters. We use the echo -n option that tells echo not to include the trailing newline in its output. We generate that text using sub-shell evaluation (an alternative to backtick evaluation) of that zcat ... command:
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Now execute cutadapt like this:. Note that the backslash ( \ ) here is just a line continuation character so that we can split a long command onto multiple lines to make it more readable.
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Now we're going to run cutadapt on the larger FASTQ files, and also perform paired-end adapter trimming on some yeast paired-end RNA-seq data.
Since batch jobs can't be submitted from an idev session, make sure you are back on a login node (just exit the idev session).
First stage the 4 FASTQ files we will work on:
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Next create a batch submission script for your job and submit it to the normal queue with a maximum run time of 2 hours.Since batch jobs can't be submitted from an idev session, make sure you are back on a login node (just exit the idev session)1 hour.
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cd $SCRATCH/core_ngs/cutadapt launcher_creator.py -j cuta.cmds -n cuta -t 01:00:00 -a OTH21164 -q normal sbatch --reservation=CoreNGS cuta.slurm showq -u # or, if you're not on the reservation: launcher_creator.py -j cuta.cmds -n cuta -t 01:00:00 -a OTH21164 -q development sbatch cuta.slurm showq -u |
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