computematrix how to set certain TSS

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.



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   # your coverage file
       -o matrix1_H3K4me3_l2r_TSS.gz  # to be used with plotHeatmap and plotProfile

before adding your answer.

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