Question: Diffbind results - non uniform width
0
2.0 years ago by
YaGalbi20
MRC Harwell Institute, Oxford, UK
YaGalbi20 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.

diffbind dba.count • 384 views
modified 2.0 years ago by Rory Stark2.8k • written 2.0 years ago by YaGalbi20
Answer: Diffbind results - non uniform width
0
2.0 years ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k 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