I have paired end RNASeq Data of 8 samples (Illumina Hi - Seq). My question is whether I should trim off the adapters from these reads before to do alignment. They provided these adapters:
a) TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3'
b) TruSeq Adapter, Index Adapter
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACXXXXXXATCTCGTATGCCGTCTTCTGCTTG 3'
If trimming is necessary, since these are paired end, does it mean I trim the Adapter-a from one of the pair (R1) and trim Adapter-b from another one of the pair? And which specific site 5' or 3' should be trimmed?
Additionally, these reads are 125bp reads, does it mean that
tophat setting "
--mate-inner-dist" should be specified as 125?
Thanks in advance!