computematrix how to set certain TSS

Question

[Binghong]

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.

Answer 1

[Friederike]

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
`

[Binghong]

thanks！so the gene. bed can only involve the gene I want instead of whole gene？

[Friederike]

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).

[Binghong]

thanks a lot !

[Binghong]

I also want to ask how can I visualize the certain gene's peaks using bed file

[Friederike]

Supply the peak file instead of the gene file