DiffBind for genome-wide promoter comparison
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mirror_hc • 0
@mirror_hc-9072
Last seen 8.4 years ago
United States

I want to use the DiffBind software to compare chip-seq intensity between different cell conditions at all promoter regions. However, I noticed that a "score" column is needed in peak files to create a dba object at the beginning. Obviously, the artificial bed files with all promoters cannot have the score column. Please let me know how you import promoter regions in DiffBind.

I tried a bed file with the score column ''.", and got the following error message:

> samples<-dba(sampleSheet="samples.csv")
MF01 J1 Reporter Negative  1 bed
Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  :
  ‘max’ not meaningful for factors

Many thanks,

Xin

diffbind • 1.2k views
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Entering edit mode
Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 8 weeks ago
Cambridge, UK

Hi Xin-

Try:

> samples<-dba(sampleSheet="samples.csv", scoreCol=0)

This tells DiffBind that there are no scores. Note that everything will get an identical score of 1, so clustering/PCA plots won't be very interesting until you get read-based scores using dba.count().

Cheers-

Rory

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