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.
You probably want the reference-point mode as described here.
You will also need a bed or 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
`
thanks！so the gene. bed can only involve the gene I want instead of whole gene？
The gene.bed file should contain the full gene region(s). computeMatrix will infer the TSS based on the genome position and the strand, i.e. for a gene on the plus strand, it will use the genome location in the second column (when TSS is the desired reference point).
thanks a lot !
I also want to ask how can I visualize the certain gene's peaks using bed file
Supply the peak file instead of the gene file
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