Overrepresented Sequences Question

Question

[Tonyzeng]

HI, I have paired end sequences, when I do QC on my reverse sequences, it showed possible source as " Illumina Single End PCR Primer 1 (100% over 30bp)" however, my forward sequences are totally good.

My question is that usually we say we need to cut overrepresented adapt sequences, here in my case, it is Illumina Single End PCR Primer 1, Do I need to do trim on them?

Answer 1

[Devon Ryan]

It's best to trim those sequences off. Use a trimmer like trim_galore or timmomatic, both of which can deal with paired-end reads. At the same time, you can quality trim to remove low quality bases from the 3' end and also set a minimum size for the trimmed reads. The trimming will generally increase your mapping rate and likely decrease incorrect mappings.