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Question: Diffbind results - non uniform width
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gravatar for kennethcondon2007
6 months ago by
kennethcondon200710 wrote:

Hi all,

I am running diffbind using narrowPeaks output from macs2

When using dba.count, I am taking each summit and counting reads +/-250 from the summit so I'm expecting to see in the diffbind report that the width column only contains "501"

bindingmatrix <- dba.count(dbaobject, summits=250) # summit +/- 250 bases

However, around 2% of the rows in the report contain a range of widths up to ~1400

Can anyone explain why this is?

Thank you.

ADD COMMENTlink modified 6 months ago by Rory Stark2.1k • written 6 months ago by kennethcondon200710
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gravatar for Rory Stark
6 months ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

If any of the 501bp intervals overlap (by at least one base), they will be merged into a wider peak. The 1400bp intervals would have been created because there are three peaks quite close together.

If you want to differentiate between very narrow peaks quite close together, you can set the summits parameter lower (100 or even 50).

Cheers-

Rory

ADD COMMENTlink written 6 months ago by Rory Stark2.1k

Thank you once again Rory :)

ADD REPLYlink written 6 months ago by kennethcondon200710
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