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Question: deepTools computeMatrix sorted values WITH gene identifiers
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gravatar for bicocca
21 months ago by
bicocca • 10
bicocca • 10 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

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modified 21 months ago by Devon Ryan • 1.9k • written 21 months ago by bicocca • 10
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gravatar for Devon Ryan
21 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

You want the list of sorted regions, which should include the gene name.
ADD COMMENT • link written 21 months ago by Devon Ryan • 1.9k
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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 REPLY • link written 21 months ago by bicocca • 10
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