how to trim only the quality scores in fastq file

Question

[vp]

Hey guys,

I have been given the fastq files of a project I have been working on from a sequencing facility but I see that the length of the sequences is shorter that the quality scores. I am guessing that they trimmed primers and adapters but they did not trim the base scores. The difference is always 16 characters. Did anyone experienced that before as well? Would you happen to have a fix for that? Ideally I would like to run a bash script and remove the 16 first characters from the quality score line and keep the rest the same. Thanks a lot for your time and help!

Answer 1

[Asaf]

You should really ask for the service to send you proper files. You can't tell what they did with it

[ATpoint]

Did they provide md5 checksums? If so check if file integrity is ok or if things got corrupted during data transfer.