Removing duplicate reads for tophat?

hong_sunwoo · 10-08-2010, 09:58 AM

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 · 10-08-2010, 10:25 AM

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 · 10-09-2010, 01:46 AM

Thanks shurjo!

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10-08-2010, 09:58 AM	#1
hong_sunwoo Member Location: Suwon, Korea Join Date: Jan 2010 Posts: 11	Removing duplicate reads for tophat? 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!!

10-08-2010, 10:25 AM	#2
shurjo Senior Member Location: Rockville, MD Join Date: Jan 2009 Posts: 126	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

10-09-2010, 01:46 AM	#3
hong_sunwoo Member Location: Suwon, Korea Join Date: Jan 2010 Posts: 11	Thanks shurjo!