Sorting .bed file by genes size
0
0
Entering edit mode
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.

Thanks in advance!

sorting chip-seq • 254 views
ADD COMMENT
2
Entering edit mode

Add the genes size (from bed or gff file) to you annotated file then sort it.

ADD REPLY

Login before adding your answer.

Traffic: 1553 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6