Question

how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind

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Laura • 0

@5cec3508

Last seen 2.5 years ago

Austria

Hello everybody, I would like to do a heatmap of selected genes for my ATAC-seq data. When I use DiffBind and I do dba.PlotHeatmap of my differentially accessible regions I get a full heatmap of all the regions and all my samples. Is it possible to show only the heatmap for specific genes maybe by specifing the region around TSS? (for e.g. -1000bp,+500bp) Thank you

DiffBind • 1.2k views

ADD COMMENT • link updated 2.5 years ago by Rory Stark ★ 5.1k • written 2.6 years ago by Laura • 0

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I have the same question, have you found a solution yet? if you havent, let me know when you do. Thanks. Regards, Team Smokekitchen

ADD REPLY • link 2.6 years ago willmane023 • 0

score 0 · Answer 1 · 2021-10-01

I suspect the dba.plotProfile() function would be more appropriate for this. Here's a workbook showing how it works:

https://content.cruk.cam.ac.uk/bioinformatics/software/DiffBind/plotProfileDemo.html

The trick would be if the differential ATAC regions are not the same as the gene regions you want. In that case, you can provide a consensus peakset with the areas around the TSSs of interest.