Question: Flip the heatmaps of ChIP-seq data to match TSS of +/- strand in deeptools
0
gravatar for Sho
22 days ago by
Sho0
Sho0 wrote:

Hello everyone,

I'm now making heatmaps from ChIP-seq data to see the tendency of where transcription factors(TFs) bind. I have a list of promoter regions(10bp to 2000bp) including chr, start and end. (start < end)

When I plotted ChIP-seq data into these regions, the pattern of heatmaps looked symmetrical because + strand promoter's TSS is on the right side of the regions, and - strand promoter's TSS is on the other side.

So I'd like to flip the - strand promoter regions such that TSS of all the regions can be seen on the right side of the regions. I can separate the regions into + and - strand regions, but I don't know how I can merge and plot them.

Is there anyway I can do this?

Thanks for your help.

chip-seq • 120 views
ADD COMMENTlink modified 18 days ago by Devon Ryan97k • written 22 days ago by Sho0
1
gravatar for Devon Ryan
18 days ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

Just include the strand in the normal position (column 6) and this will be done automatically by deepTools.

ADD COMMENTlink written 18 days ago by Devon Ryan97k

It worked! Thank you!

ADD REPLYlink written 16 days ago by Sho0
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