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!

 
 

The 3' ends of the reads should be trimmed.

Tophat mate-inner-dist is the distance bet the 2 reads of a pair, and depends on the average fragment length, you should obtain an idea of that value from the sequence provider, or whoever did the library prep.

