We did a RNAseq paired end with 150 bp in NovaSeq with TruSeq Total RNA strandred, with an external supplier. I'm now trying to analyze the data but I'm having trouble with the adaptors
They sent me the following sequences:
But I'm not entirely sure how I should use this in cutadapt
With the manual of illumina (https://support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html), I should remove both of them in the 3', but I'm not sure if p7 is for read 1 and p5 is for read 2, if I should remove both adapters from both ends of read 1 and 2 etc.
Maybe I should ask them, but I want to be sure what I need to ask so I can obtain the correct answer
Also, is it bad to remove both sequences from both ends of the 2 reads? Why?