Different Sequence Length Distribution between forward and reverse reads

Question

[Linda]

Hi! I'm a new to trimming and QC of fastq files. I have human WES fastq files (reverse and forward) and ran FastQC on them and the adapters have already been trimmed by the sequence provider. For all the individuals, the sequence length distribution for the forward and reverse read lengths are similar ~100, but for 2 individuals, the sequence length distribution for the forward reads is ~100 and for the reverse reads is ~50. My question is: is it normal to have such drastically different sequence length distributions for the forward (~100) and reverse (~50) reads?

Thank you in advance!

Answer 1

[GenoMax]

That does not seem normal. If all samples were part of a pool and ran on the same flowcell then that likely discounts sequencing issues with the two libraries. Only possibility I see is the reads may have been quality trimmed (in addition to adapters). I would suggest that you ask for original data from the sequence provider and scan/trim it yourself. Perhaps you will end up with a different result.

[Linda]

Thank you for your answer!

I will see what I can do.