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Hard clip fastq

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.

fastq
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updated by GenoMax GenoMax • written by samuel samuel

2 answers

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

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written by ATpoint ATpoint

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

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written by samuel samuel

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

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written by GenoMax 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
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written by GenoMax GenoMax

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