multiBigwigSummary with outRawCounts - output all fields from input bed

[António Miguel de Jesus Domingues]

Hi all,

I am using the` multiBigwigSummary --outRawCounts` to retrieve the coverage for several BigWigs, and over a large number of BED files. These bed files contain an ID on the forth column which is necessary for downstream processing (grouping, averaging, etc). However, I noticed that the output bedcontains only the first three fields from the input BED. Is it possible to include in the output bed all the fields of the input?

I guess I could convert the BigWigs in Bedgraph and used bedtools map for this, but I would rather not have another file format converstion.

Command used:

multiBigwigSummary BED-file -b $bws -o coverage.npz --BED random_${i}.bed --outRawCounts random_${i}_coverage.tab --smartLabels -p 6

(I realized this might be more a feature request than a question but there you go)

Cheers,

António

[Devon Ryan]

Hi Antonio,

Unfortunately the --outRawCounts option is quite simplistic, so it
won't provide what you want. You could probably hack this
functionality in by editing countReadsPerBin.py (the
counts_reads_in_region function), but the exact changes that are
needed aren't immediately apparent to me so it'd require some playing
around.

Devon


--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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[Antonio Miguel de Jesus Domingues]

Hi Devon,

thank you for point me in the direction of the solution. In the meantime I thought of a couple of workarounds so this hack might not even be needed, but now I know where to look.

Cheers,
António

-- 
------------
António Miguel de Jesus Domingues, PhD

Bioinformatics Data Analyst @ MPI-CBG