Question: Flip the heatmaps of ChIP-seq data to match TSS of +/- strand in deeptools
0
gravatar for Sho
3 months 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 • 229 views
ADD COMMENTlink modified 3 months ago by Devon Ryan98k • written 3 months ago by Sho0
1
gravatar for Devon Ryan
3 months ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

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

ADD COMMENTlink written 3 months ago by Devon Ryan98k

It worked! Thank you!

ADD REPLYlink written 3 months ago by Sho0
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