In which end trim adapters

Question

[jimenezs]

Hello,

I'm sorry for the stupid question, I'm a bit confused.

If my reads were originated from the first cDNA strand and therefore they are in the reverse strand compared to the transcribed one. The trimming of the poly-A and the Illumina adapter should be done on the 5' end?

I would really appreciate your comments :)

Have a nice day!

[GenoMax]

It is unlikely that you will have Illumina adapter sequence on 5'-end. Way illumina sequencing primer works you read into your sequence with first base. If you have adapter dimers (i.e. no insert) then that would be the time you will see adapter sequence right away.

Answer 1

[JC]

Check them with FastQC to visualize if you need to trim and where.

Answer 2

[swbarnes2]

I don't think this can be answered without knowing more about how your library prep actually works, but you shouldn't have adapter between your sequencing primer and your sequence of interest. You likely aren't trying to sequence through the whole poly-A tail to get to your sequence of interest either