computematrix how to set certain TSS

computematrix how to set certain TSS

1

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.


deeptools

• 55 views

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
`


Login
before adding your answer.

Source link