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?
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
If you simply want the reads to be compatible in length then do not adapter trim.