I have >500 fastq.gz files from a RNASeq project and was told they have been run with either 125bp or 50bp. I am wondering if there is a quick way to check which files are 125bp and which are 50bp. One file seems not bad to check but for 500 files I wanted to find a better way.
testformat.sh from BBMap suite.
$ testformat.sh file.fq.gz
sanger fastq raw single-ended 118bp
Or to test all files with one command:
testformat.sh *.fq
Only caveat is it does not recognizes separated paired files as paired, but this will have no effect for what you want to do.
edit: sorry, just noticed it doesn't output file name. A solution would be something like:
for i in *.fq
do
echo $i; testformat.sh $i;
done
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Although there might be a solution which does what you want... This shouldn't be too hard to write a custom script for, do you have any experience with that? I would write it in python, but that's a personal preference.