Sorting .bed file by genes size
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6 months ago
Marco Pannone ▴ 240

Hello!

I have a .bed file from the peak calling analysis performed with MACS2 for ChIP-seq data. I have annotated the peaks in this .bed file to nearby genes.

I am looking for a way to order the peaks based on the size of the nearby genes they have been annotated to. I need to do that in order to produce a final heatmap where all the genes are reported in descending size order.

So, in case I can do the ordering already for the .bed file, then use it as input to computeMatrix with --sortRegions keep and then plotHeatmap with --sortRegions no.

sorting chip-seq • 254 views
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Add the genes size (from bed or gff file) to you annotated file then sort it.