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Visualize coverage across exons with varying lengths

Hi,

I have per base read depths for a bunch of exons with different lengths. I want to plot the read depth for these exons in the same graph. Can someone please tell me how to divide the read depth values into 100 bins for every exon. So I can have an x axis from 0 to 100. I want to see coverage across exons. My problem is the exons are different length from 35bases to 4000bases. I have read depth for each base (most are zero).

Thank you in advance

exons python readdepth binning
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updated by Friederike Friederike • written by Kash Kash

there are plenty of functions out there that will deliver you a moving average; alternatively need to just write a custom script for this.

do you have a bam file? if so, can use IGV.

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written by LauferVA LauferVA

2 answers

I wrote http://lindenb.github.io/jvarkit/WesCnvSvg.html

enter image description here

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

deepTools' computeMatrix and plotProfile may do what you need. You'd need a BED file of exons and a bigWig file of read coverages, though

see here

• 0 views • link
written by Friederike Friederike

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