computematrix how to set certain TSS
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18 months ago
Binghong ▴ 20

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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18 months ago

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

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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).

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thanks a lot !

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

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Supply the peak file instead of the gene file

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