diffbind and macs2 output
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tony ▴ 10
@tony-9402
Last seen 5.9 years ago

I would like to know how to format the macs2 peaks to be used in diffbind package. I have the following files:

omodel_model.r
omodel_peaks.broadPeak
omodel_peaks.gappedPeak
omodel_peaks.xls

I can not use the xls as I am getting an error:

Error in Summary.factor(c(926L, 1085L, 1022L, 998L, 902L, 1360L, 677L,  :
  ‘max’ not meaningful for factors

The contents of xls file are:

chr     start   end     length  pileup  -log10(pvalue)  fold_enrichment -log10(qvalue)  name

Thanks in advance.

 

 

 

diffbind macs2 • 3.5k views
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Gord Brown ▴ 640
@gord-brown-5664
Last seen 9 months ago
United Kingdom

Hi,

When you use the "--broad" option, the .xls output format is slightly different from the usual MACS format (missing the "summit" column).  DiffBind doesn't account for that, unfortunately (though I'll put it on the to-do list).

The "broadPeak" and "gappedPeak" formats are almost "bed" format; just use the first 6 columns only, and rename them to have a ".bed" suffix.  This command will extract the first 6 columns:

> cut -f 1-6 something.broadPeak > something.bed

Hope this helps...

 - Gord

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(And change your sample sheet to show that the files are 'bed', not 'macs' format)

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Hi,

17 months later does Diffbind handles .xls format from MACS2 --broad option ? or do we still have to use your trick ?

Just to know , thanks !

Edit : Seems to work using macs in Peaks Column

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hello! 

if i want to analysis broadpeak ,can i use this file ---macs.xls? and select 'macs' format in the samplesheet now? 

thanks

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