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CompEpigen / figeno

Tool for plotting sequencing data along genomic coordinates.
GNU General Public License v3.0
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Make sure that the region that you specified does not extend beyond thechromosome length, and that you did not subset your .cool file. #17

Closed makou1213 closed 2 months ago

makou1213 commented 2 months ago

Hello author, why am I following the normal process, but the following prompts appear: Could not retrieve region Chr1:0-200000 in file F:\hic-data\KJ.25000.iced.matrix.cool. Make sure that the region that you specified does not extend beyond thechromosome length, and that you did not subset your .cool file. I used the custom mode and uploaded the gtf file.

e-sollier commented 2 months ago

Hi,

Thanks for your interest in figeno, and sorry for this bug. I suspect the issue might be the capital letter in Chr1. Could you try replacing Chr1 with chr1 and let me know if this works? If yes, then I will update figeno to better handle capital letters in the chromosome names. Otherwise, would you be able to share the .cool file so that I can investigate?

You can also try using a narrower window, e.g. chr1:500000-1500000 and see if this helps?

makou1213 commented 2 months ago

Thanks for your reply. I tried to change it to lowercase, but it still doesn't work. My chromosome is not human, can I send the .cool file to you by email?

e-sollier commented 2 months ago

Yes sure you can send the cool file by email (etienne[dot]sollier[at]dkfz[dot]de).

makou1213 commented 2 months ago

Hi, the email has been sent. Please check your inbox. Thanks.

e-sollier commented 2 months ago

Thanks for sharing the .cool file. It turns out that the .cool file does not contain balancing weights for normalization, whereas figeno was assuming that these weights were present. If you run cooler balance /path/to/your/file.cool, and then generate the figure with figeno, this should work. See https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance for more information.

I will update figeno to better handle cases when these weights are missing.

Edit: in version 1.3.3, figeno will now plot the raw data if balancing weights are not available, and show a warning.

Also, for your sample you should use Bomo_Chr1 for the chromosome name (if you want to show chromosome 1)

makou1213 commented 2 months ago

It is now up and running! Thank you for your guidance!