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ay-lab / mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
MIT License
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error loading a .mcool file #62

Open alexandremarcil opened 2 months ago

alexandremarcil commented 2 months ago

Hi,

I am trying to run mustache on a publicly available dataset, but I keep getting an error:

python3 ~/code/mustache/mustache/mustache.py -f GSE130275_mESC_WT_combined_2.6B.mcool -pt 0.1 -o ES_loops_200.tsv -r 200 -p 10

KeyError: "No cooler found at: GSE130275_mESC_WT_combined_2.6B.mcool. Coolers found in ['/0', '/1', '/2', '/3', '/4', '/5', '/6', '/7', '/8', '/9', '/10', '/11', '/12', '/13', '/14', '/15', '/16', '/17']. Use '::' to specify a group path"

It seems this file does not have the various resolutions stored as ::/resolutions/...
Is there a way to correct the file format? Is there a way to load this file with mustache and diff_mustache?

Here is the file in question: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130275

Thanks!

cemilcan98 commented 2 months ago

Hi,

You can run mustache on your data using the .hic file provided in your link rather than the .mcool file with the following code:

python3 {path_to}/mustache.py -f {path_to}/GSE130275_mESC_WT_combined_2.6B.hic -pt 0.1 -o ES_loops_200.tsv -r 200 -p 10

The error you are running into has to do with the .mcool format and you can find more about that discussion here: https://github.com/XiaoTaoWang/NeoLoopFinder/issues/15

Using the .hic file for both mustache and diff_mustache should be better or you can follow the discussion in the GitHub link provided above.

I hope this helps.