Paired-End RNA Seq Trimming Workflow

Hello Galaxy Community,

I am trying to educate myself on this NGS thing. Have some questions regarding my data, paired-end RNA seq. So I have mouse tissue, from Knockout and Control animal, 4 biological replicates for each. They were prepared using TruSeq Kits Single Index. I read on the Illumina page (TruSeq Single Indexes ) that for trimming, I only need these following sequence:

Read 1

Read 2


  1. Should I use those 2 sequences for all my data sets?
  2. Or do I need only to trim the index sequence, like 6 bp? I know the index sequence for each sample. But it seems inconvenience if I do trimming for all my datasets at onceā€¦
  3. The aim of my sequencing is to know the differential gene expression from knockout vs. control as well as to identify splice variants. Is trimming still necessary? Because I read in some discussions for that aim, and if I align it with RNA STAR, trimming is not necessary anymore.

I highly appreciate your help :hugs: