Diffbind results - non uniform width
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YaGalbi ▴ 20
@yagalbi-11519
Last seen 2.0 years ago
MRC Harwell Institute, Oxford, UK

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.

diffbind dba.count • 584 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 18 days ago
CRUK, Cambridge, UK

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

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Thank you once again Rory :)

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