Computematrix input wig file

[luckysardar]

I am new to deeptools and chipseq data analysis , Wanted to plot density TSS and genebody using computematrix and plotprofile, the wig file which is needed for compute matrix is it bam (mapping file) to wig file or after peak calling I can get one wig or bed file(macs2 peak caller). Little bit confused Which is prepared file to use please help me

Thank you

[dpryan79]

You'll want a bigWig file for the entire genome. See bamCoverage for an example of how to make a bigWig file.

[luckysardar]

Thanks for quick reply I have BigWig file for entire genome. I am using computematirx for my gene of interest for that I have used directly GTF file filtered(according to gene of interest) it gave me error so I converted GTF file bed file(chr, strat,end, genename) and run the Computematrix it ran with some error like

A region that is shorter than the bin size (possibly only after accounting for unscaled regions) was found: (3) 7:107209509-107209512 7:107209509:107209512. Skipping...

Skipping 7:107209509-107209512, due to being absent in the computeMatrix output.

command I have used bamCoverage -b sample1.bam -o sample1.bw --normalizeUsing BPM --ignoreDuplicates -p 6

After the below command I got above errors

computeMatrix scale-regions -S sample1.bw -R gene_ofInterest.bed -a 5000 -b 5000 -o Samples.matrix --regionBodyLength 15000

Can you please help me is it ok to get this kind of things or is there any way I can resolve this

[dpryan79]

That's a 3 base long region, so you're going to have issues with it. Did you artificially truncate it? You likely want reference-point instead of scale-regions if so.

[luckysardar]

Thank you, my data is from pol2 for gene body is looking fine I am observing enrichment in genebody from above command, for TSS region middle of plot promoter region we should observhttps://github.com/luckysardar/plotsdata/blob/main/plII.pnge high peak, I am not getting like that can you please suggest me how to run it for TSS i have run using reference-point and scale-regions from both I am getting same kind of plots or there is problem in my data can you suggest me.

computeMatrix reference-point --referencePoint TSS -b 2000 -a 2000 -R genes.bed -S plII.bw -p 6 -o Samples.matrix.tss plotProfile -m Samples.polII_matrix.tss -out plII.png

plot