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!
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.