Size of chr2 and chr3 incredibly small for mouse data

colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data

GNU General Public License v3.0

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Size of chr2 and chr3 incredibly small for mouse data #19

Closed Urja25 closed 3 months ago

Urja25 commented 8 months ago

Hi,

when I run epiAneufinder on mouse data, I get a karyogram with very small sizes for chr2 and chr3 especially amongst other chromosomes. Could you help me correct the sizes?

e.g.

Thanks a lot!

thek71 commented 8 months ago

Hi,

I think that what happens is that many bins in chr2 and 3 are filtered out due to lack of coverage. If you are running epiAneufinder with default settings, then bins for which 85% of the cells have no signal are filtered out. To verify that you can check on the results.tsv file and see for how many bins in the chromosomes 2 and 3 there is CNV information. Only these bins are plotted.

Best, Katia