Entering edit mode
16 months ago
Marco Pannone ▴ 710
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
--sortRegions keep and then
Thanks in advance!
Add the genes size (from bed or gff file) to you annotated file then sort it.