Question

diffbind and macs2 output

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tony ▴ 10

@tony-9402

Last seen 7.3 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 • 4.1k views

ADD COMMENT • link updated 7.3 years ago by Gord Brown ▴ 650 • written 7.3 years ago by tony ▴ 10

score 1 · Answer 1 · 2015-12-21

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Gord Brown ▴ 650

@gord-brown-5664

Last seen 2.2 years 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

ADD COMMENT • link 7.3 years ago Gord Brown ▴ 650

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

ADD REPLY • link 7.3 years ago Gord Brown ▴ 650

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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

ADD REPLY • link 5.8 years ago ZheFrench ▴ 40

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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

ADD REPLY • link 4.3 years ago 1692679247 • 0