Deeptools: computeMatrix can't read file

Question

[yomogy]

Hi,

I generated bigwig file using bamCoverage with the following code.

bamCoverage -b A.bam -o A.bw --binSize 10 -p max --normalizeUsing CPM

Then, I tried to use computeMatrix

computeMatrix -S A.bw -R B.bw -o C

but I got the following error

usage: computeMatrix [-h] [--version]  ...
computeMatrix: error: argument : invalid choice: 'A.bw' (choose from 'scale-regions', 'reference-point')

I am wondering whether anybody had similar problems.

Answer 1

[GenoMax]

An example usage is:

  computeMatrix scale-regions -S <biwig file(s)> -R <bed file> -b 1000

You need to include 'scale-regions' OR 'reference-point' before your options.

[yomogy]

Thanks, it works.

[adR]

Hi GenoMax, I have these bigwing files and want to run computeMatrix but could not understand what -R <bed file>. would please explain me what is this -R <bed file> and where I can find it? Thank you so much for your help! best, ad

[GenoMax]

Those are regions you want to compute the matrix for in BED or GTF format.

[adR]

Thanks ! But to get those files I am suppose to convert the Reference Genome Annotation in gff3 to bed?

[GenoMax]

As the manual indicates:

Typically, the genome regions are genes, but any other regions defined in a BED file can be used.