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Old 10-08-2010, 09:58 AM   #1
Location: Suwon, Korea

Join Date: Jan 2010
Posts: 11
Default Removing duplicate reads for tophat?


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?

hong_sunwoo is offline   Reply With Quote
Old 10-08-2010, 10:25 AM   #2
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 is offline   Reply With Quote
Old 10-09-2010, 01:46 AM   #3
Location: Suwon, Korea

Join Date: Jan 2010
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Thanks shurjo!
hong_sunwoo is offline   Reply With Quote

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