cooler/higlass for capture Hi-C data

Hi guys,

I was trying to analyse capture Hi-C data with cooler/higlass but I’m facing a couple of issues. Let say I have a Hi-C map on chr1 from range A to B. I processed the data with HiC-Pro and I have now a sparse text format with bin1/bin2/count and a bin file from A to B.

cooler load -f coo --one-based CAPTURE.bed CAPTURE.mat CAPTURE.cool

works well. However, when I try to zoomify with

cooler zoomify --balance CAPTURE.cool -r 5000,10000,20000,40000

It crashes with cooler.create._ingest.BadInputError: Found a bin ID that exceeds the declared number of bins. Check whether your bin table is correct.

I guess this is because when I zoomify, I’m going outside the range of my A-B capture.

Note that if I’m doing the same with the whole chromosome size, it works. However, as soon as I normalize, the higlass output is empty, I have no map. So in theory, I would like to run the normalization of my capture region only, and the fact that I have the whole chromosome may explain why there is nothing in higlass.

Therefore, I normalized the data by myself and try to build a cooler file but I have TypeError: Cannot cast array from dtype('float64') to dtype('int32') according to the rule 'safe' But I though that this issue of floating value was already fixed ?

Any idea is welcome. Best Nicolas

[nservant]

done https://github.com/mirnylab/cooltools/issues/176

[nservant]

Hi, Indeed, sorry, it was my fault. I made a mistake in the resolution. It works now ! And your command also works.

>>cooler dump -t bins --header CAPTURE.mcool::resolutions/10000 | head
chrom	start	end
chrX	0	10000
chrX	10000	20000
chrX	20000	30000
chrX	30000	40000
chrX	40000	50000
chrX	50000	60000
chrX	60000	70000
chrX	70000	80000
chrX	80000	90000

Thanks guys for the quick support. I’m closing the issue. N