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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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Two questions; about 'Cell_type_noise' filter and MT mutation calling #41

Open leehs96 opened 8 months ago

leehs96 commented 8 months ago

Hello,

I hope you're doing well. I'm currently working with 3'-10X chromium scRNA data, and I have a couple of questions regarding the filtering steps.

'Cell_type_noise' filter: I would appreciate it if you could provide more details on the meaning of the 'Cell_type_noise' filter. My understanding is that it might be related to mutations detected across several cell types, but I noticed it's annotated with the name 'Multiple_cell_types.' Could you clarify the exact significance of 'Cell_type_noise' in this context?

Alternative filtering for MT mutation calling: I'm particularly interested in understanding MT mutation accumulation in specific cell types in the context of cancer. Considering this, I'm a bit unsure whether I need to adjust the filtering criteria from the examples provided. Do you have any recommendations for filtering criteria specifically tailored for MT mutation calling in this scenario?

I would greatly appreciate any insights or recommendations you could share. Thank you in advance.

nikonovaelizaveta commented 4 months ago

I would also like to get clarification on filters. Could you please post the meaning of each of the filters.