Sequence length and quality length are different in fastq file

Question

[miles.anderson]

I'm doing a whole genome alignment and I get an error when using samtools that my sequence and quality length differ, but it doesn't tell me at which reads.

Is there anything specifically that can cause this when doing read trimming? I used bbduk to trim my reads.

Thanks

Answer 1

[GenoMax]

That is a sign that your data is corrupt in some way. It is less likely that bbduk.sh caused this so the original files may be that way. Use one of the answers to identify the problematic reads and remove them: Checking fastq is valid

[miles.anderson]

Hmm. I ran the awk command from the post and it returned 0 for both read files. I processed the files again through bbduk with a trim quality of 10 instead of 15. I'll see if they map correctly this time.

Could it have been an issue with bowtie2?