Removing duplicate reads for tophat?

[hong_sunwoo]

Hello.

I have two human single end RNA seq data generated from Solexa.
Yesterday, I ran fastqc using my data and the program reported that two data have a little amount of duplicated reads.

Should I remove this before processing Tophat?
And is there any programs which can be used for such purpose?

Thanks!!

[shurjo]

A small amount of duplication is going to be present in almost any RNA-Seq library. I would not remove these before running TopHat or any other aligners.

There are threads on this forum where this issue has been discussed in great detail, inncluding one which has a link to a mathematically rigorous treatment of the question by lh3, a senior user. Searching the forum with "duplicate reads" should point you in the right direction.

Best of luck,

Shurjo

[hong_sunwoo]

Thanks shurjo!