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uio-bmi / graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome
BSD 3-Clause "New" or "Revised" License
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Any way to render the peaks on top of a graph? #6

Open cgroza opened 5 years ago

cgroza commented 5 years ago

Hi, It is already possible with vg to visualize graph alingments onto the graph itself. Do you know of any way of taking the peak annotations produced by Graph Peak Caller and including them in the same graph alignemnt visualization?

In your paper, you show how a peak can lay on top of a path: https://journals.plos.org/ploscompbiol/article/figure/image?size=large&id=info:doi/10.1371/journal.pcbi.1006731.g001

This is essentially what I am trying to reproduce.

My thanks.

ivargr commented 5 years ago

Hi!

There are nice ways to visualize alignments with vg (https://github.com/vgteam/vg/wiki/Visualization), but for now I unfortunately don't know of any good way to convert the peak intervals (Offsetbasedgraph intervals) to vg alignments. The figure you linked to is just drawn manually. We have written code for converting from vg to Offsetbasedgraph, but not the other way around. However, it should not be to tricky to convert to the vg alignment json format, and then use vg to visualize. If you only have a small handful of peaks you want to visualize, you could also just write them in the vg json format manually.