strand information ComputeMatrix

[Elena Gómez-Díaz]

Hello,

I now this is a naive question but I would like to make sure I am doing things right.
When computing the matrix for the heatmap, does the ComputeMatrix tool take into account strand information in defining TSS and TES if this is defined in the bed file (edit attributes option) or one must flip coordinates before uploading the bed reference file?

Thanks!
elena

[Friederike Dündar]

Hi Elena,

great to see you find many uses for deepTools!

If the strand is in the 6th column (as it should be the case in a normal BED file), computeMatrix will take it into consideration.

Best,

Friederike

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[Elena Gómez-Díaz]

Hi again,

Is still related with the ComputeMatrix and the Heatmapper tools. I found an issue when you have genes that are very close together and you want to map the enrichment profiles of scaled gene regions PLUS a flank region of certain lenght.
Did somebody have had similar issues? Any advice on how to overcome this problem? Or it is just only mapping the gene?

thanks once again

[Friederike Dündar]

Hi Elena,

I'm not sure if I understood you correctly - do you see an error reported by computeMatrix? Or are you just concerned about how computeMatrix handles close-by, possibly overlapping genes?

Perhaps the answer in the FAQ section is what you're looking for:
https://github.com/fidelram/deepTools/wiki/General-deepTools-FAQs#compMatrix_overlap

If this doesn't help, please explain the issue you're experiencing in more detail.

Good luck!

Friederike