Hard clip fastq

Question

[samuel]

I hope this is not a silly question. I have 2x 200bp fastqs generated from MGI G400 sequencer.

I would like to do a comparison with Illumina but these only come as 2x 150bp fastqs.

Is it possible to hard clip the 2x 200bp fastqs down to 2x150bp in order to do this comparison? If so, would this have to be done AFTER adapter trimming? Also, if it is possible, what is the recommended tool to use?

Many thanks.

Answer 1

[ATpoint]

Use seqtk trimfq. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.

https://github.com/lh3/seqtk

[samuel]

@ATpoint, so no adapter trimming first? Just trim the raw fastq?

[GenoMax]

If you simply want the reads to be compatible in length then do not adapter trim.

Answer 2

[GenoMax]

You can also use reformat.sh from BBMap suite as follows

reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz out2=R2_trim.fq.gz forcetrimright=50