Hi everyone, I have a count matrix from feature counts and of course, couple of peak (.bed) files. I want to visualize the peaks all together to show the coverage and overall comparing. I was going to use plotprofiles and plotheatmap of computeMatrix tool of deeptools, but it needs its own made countmatrix, which chaines to using other tools of deeptools including binning the genome with bamcoverage and stuff. For some reason, I'm unable to use computematrix tool of Deeptools, it gives me lots of errors. I think, I'm not quite sure how should be files. I have coordinates of peaks, should I annotate them first? But even if I use annotated version, it again stops. Besides, it never accepts my .bw file that I already have made with Bamcoverage from bam files of the same replicate that I called the peaks and now I'm trying to visualize it.
Can anyone please send me the structure (sample) of computed matrix of this tool so I can re-structure my featureCounts matrix and use that instead? Thanks so much.