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title	Answer

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:

Code Block

language	bash

echo -n $( zcat Sample_H54_miRNA_L004_R1.cat.fastq.gz | head -2 | tail -1 ) | wc -c

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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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title	Setup (if needed)

Code Block

language	bash
title	Setup for cutadapt on miRNA FASTQ

export CORENGS=/work/projects/BioITeam/projects/courses/Core_NGS_Tools
mkdir -p $SCRATCH/core_ngs/fastq_prep
cd $SCRATCH/core_ngs/fastq_prep
cp $CORENGS/human_stuff/miRNA_test.fq .

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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.

Code Block

language	bash
title	Create and submit cutadapt batch script

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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