Question: deepTools computeMatrix sorted values WITH gene identifiers
gravatar for bicocca
14 months ago by
bicocca10 wrote:

I've performed a computeMatrix analysis on a ChIP-seq sample referenced to gene TSSs. This generates a list that can be turned into a heatmap, sorting genes with highest signal to lowest signal. However, I can't figure out how to retain the gene ID information with the computeMatrix values. The accompanying "Heatmap values" are just a series of values without any gene identifier. The heatmap LOOKS nice, but has limited value if I can't identify the genes along the Y-axis. Is there someway to export or generate a bed (or similar) file with sorted gene info? Thanks

chip-seq • 456 views
ADD COMMENTlink modified 14 months ago by Devon Ryan1.9k • written 14 months ago by bicocca10
gravatar for Devon Ryan
14 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

You want the list of sorted regions, which should include the gene name.

ADD COMMENTlink written 14 months ago by Devon Ryan1.9k

Answer: In "advanced output settings" make sure the "Save the regions after skipping zeros or min/max threshold values" is checked "yes". It will generate a second file with the desired sorted regions.

ADD REPLYlink written 14 months ago by bicocca10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 73 users visited in the last hour