Quick check of the RNASeq length for a bunch of files

Question

[ddzhangzz]

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.

[WouterDeCoster]

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.

Answer 1

[GenoMax]

testformat.sh from BBMap suite.

$ testformat.sh file.fq.gz 
sanger  fastq   raw single-ended    118bp

[h.mon]

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

[GenoMax]

for i in *.fastq.gz; do echo $i | tr '\n' '\t' ; testformat.sh $i ; done