Question: rmdup - remove PCR duplicates from ChIP-seq data
0
gravatar for david.fear
4.1 years ago by
david.fear10
European Union
david.fear10 wrote:

I have aligned my chip-seq data with bow tie and wanted to remove PCR duplicates. I ran rmdup in SAM tools on the aligned file but the number or reads I got back (i.e.. 8787256 / 9006759 = 0.9756 in library) was more than the number of single aligned reads I started with? I assume these numbers are number of unique reads vs total reads tested, is this correct?

 

Many thanks

Dave

samtools chip-seq • 4.3k views
ADD COMMENTlink modified 4.1 years ago by Jennifer Hillman Jackson25k • written 4.1 years ago by david.fear10
1
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

The tool you are looking for is "NGS: Picard (beta) -> Mark Duplicate reads".

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for david.fear
4.1 years ago by
david.fear10
European Union
david.fear10 wrote:

Hi,

Thanks for your reply, how is this different from rmdup in SAM tools?

Dave

 

ADD COMMENTlink written 4.1 years ago by david.fear10
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

There is much discussion about the use these two tools. This is a good place to start: http://seqanswers.com/forums/showthread.php?t=5424

Best, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
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