PolyA in FastQC results from EM-Seq?

Question

[Watermelon]

Hello all,

I received the first EM-seq data for our samples and especially R2 have polyA sequences in the file according to FastQC results. I'm not familiar with why this could occur and the sequencing company had no answer for me. I'm hoping someone can shed a light?

Also, if you could recommend how to trim these, I would very much appreciate it. I was thinking of using TrimGalore -a2 A{20}. Would I also need to trim R1's in the same way?

[AP]

Hi,

We are encountering the same issue...after trimming (using fastp with default settings), R2 has a polyA content according to fastqc report...

Any suggestions for trimming? Is it related to conversion?

Many thanks!

[Ram]

P.S: Please do not add answers unless you're answering the top level question. Instead, use Add Comment or Add Reply as appropriate. I've moved your post to the right location this time, please be more careful in the future.

[sunsong2024]

I also encountered the same problem. Have you found the reason

[Watermelon]

I came to believe this is due to short fragments in the library but don't quote me on this. My solution was to trim with TrimGalore using options -a T{10} -a2 A{10} and this seems to work the best. I don't see any polyA sequences after trimming and alignment was without issue.