how MACS2 select reads for peak calling

[Louella Judy Vasquez]

Hello

May I just ask which reads does MACS2 use for peak calling?

I know that by default duplicate reads are removed.

Are multimapped reads removed  too?

Are only proper paired reads considered?

Does MACS2 filter on mapping quality of reads?

Any help is much appreciated!

Many thanks!

Louella

Sanger Institute

[Tao Liu]

Hi Louella,

Here are the answers:

On Mar 27, 2014, at 3:05 PM, Louella Judy Vasquez <kulo...@gmail.com> wrote:

> May I just ask which reads does MACS2 use for peak calling?
> I know that by default duplicate reads are removed.

Assume you were asking ‘callpeak’ function. Right.

> Are multimapped reads removed too?

No.

> Are only proper paired reads considered?

Yes.

> Does MACS2 filter on mapping quality of reads?

No.

As for BAM file, only FLAG field is checked so MACS won’t check mapping quality, multiple mapping tags and so on, because other input formats such as BED or TagAlign don’t have such information at all. It should be the pre-processing task before peak calling. So you need to tweak your aligner or write scripts if you don’t want those reads.

Best,
Tao

[Louella Judy Vasquez]

Thanks Tao!!

Louella

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