should I reverse paired end reads before mapping?

[supermario]

Hi , I am starting with tophat.

I have a paired end illumina HISeq RNA Seq dataset with two files:

SRR12331_1.fastq and SRR12331_2.fastq

should I reverse the reads files in SRR_2.fastq before mapping with tophat?

say I have a read from SRR12331_2.fastq:
TTTTGGG

should i feed tophat with :

GGGTTTT

THANKS!

[Jon_Keats]

nope leave them as they are the reads would have been generated as
-----> <-------
pairs which is the expected form by all aligners designed to deal with illumina paired-end data. The only time you may do this is with illumina mate-pair data which generates data
<------ --------->

[andyding]

You don't need to do reverse complement for the second set of read.
As Jon_Keats said, most mainstream aligners are designed to deal with Illumina paired-end reads.
I never used tophat, but I've used BWA, and it can map paired-end reads to ref seq perfectly.