computematrix how to set certain TSS
how to set certain TSS deeptools computematrix, I want to visualize the certain gene’s TSS up/downstream instead of whole gene,but how can I do it ? thanks.
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You probably want the
reference-point mode as described here.
You will also need a
gtf file with the gene regions and via the
--referencePoint parameter you specify that you want the TSS (rather than the TES or the center of the regions in the BED file).
Example code from here:
$ computeMatrix reference-point # choose the mode --referencePoint TSS # alternatives: TES, center -b 3000 -a 10000 # define the region you are interested in -R genes.bed # the gene annotation of your choice -S log2ratio_H3K4Me3_chr19.bw # your coverage file --skipZeros -o matrix1_H3K4me3_l2r_TSS.gz # to be used with plotHeatmap and plotProfile `