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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicPlotTADs error: bw file not displayed #837

Open aminakur opened 1 year ago

aminakur commented 1 year ago

I am using hicPlotTADs to simultaneously visualize hic map and chromatin marks tracks. My tracks.ini file:

[bigwig]
file = PRO-seq.bw
title = PRO-seq
color = black
min_value = 0
max_value = 30
height = 2

The .png file doesn't have the .bw tracks properly displayed:

image

I am getting the following error:

INFO:pygenometracks.tracksClass:plotting 9. [tads]
INFO:pygenometracks.tracksClass:plotting 10. [spacer]
INFO:pygenometracks.tracksClass:plotting 11. [bigwig]
WARNING:pygenometracks.tracks.GenomeTrack:*Warning*
Neither chr01 nor 01 exists as a chromosome name inside the bigwig file. No score will be computed for PRO-seq.bw.

This happened to several .bw files from various sources. I have tried other chromosomes, same error. How can I transform them to plot them with hicPlotTADs? I did not generate the .bw files, they were sent to me by a former member of my group or downloaded from NCBI.

kalavattam commented 1 year ago

Seems like you need to adjust the names of the chromosomes in the file. For one approach on how to do that, see here. General Google search results for how to do it here.

lldelisle commented 1 year ago

I think this is also something we could propose within the software. Could you tell me which species it is? and which assembly? Thanks