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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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Could this algorithm be used in Mouse data? #12

Closed RinconFer closed 11 months ago

RinconFer commented 1 year ago

Hello, I work with cancer mouse models using both scRNAseq and snATACseq datasets, I would like to use this package to detect mutations in my cancer models. Is it possible to use it in Mouse datasets?

Francesc-Muyas commented 1 year ago

Dear user, Thanks for your interest in SComatic. Our algorithm can be run in different types of species; however, there are a few limitations that need to be in consideration.

  1. SComatic has been benchmarked using Human data, so although we do not find many reasons for having worse performance, we cannot guarantee the same performance for mice or other species.
  2. As you will realise, step 4 of SComatic takes (not mandatory, but recommended) a Panel of Normals (PoN) for filtering potential germline and systematic error contamination. In the repo (as described in the manuscript), we provide a scRNA-seq PoN for the human genome. However, although we don't have the PoN for the mouse genome ready yet, we are working on it and hope it will be available in the Github repo soon.
  3. Similar to the previous point, step 4 of SComatic also takes (not mandatory, but recommended, and only for scRNA-seq data) an RNA-editing bed file with positions known to be affected by A-to-I and/or C-to-U editing events in the literature. Although the one provided in the repo is based on the human genome, we are collapsing some mouse RNA-editing databases and will upload this file to the GitHub repo soon.

You'll find these updates in the GitHub repo soon! Thanks for your interest, Fran

RinconFer commented 1 year ago

Thank you very much!

I'll wait then for the mouse PoN and the bed file.

Best, David

Francesc-Muyas commented 1 year ago

Just to let you know. We are working on it and expect to deliver these files next week.

RinconFer commented 1 year ago

That's great! Thank you! Once you upload it I'll give it a try as soon as I can and let you know how it went

Francesc-Muyas commented 11 months ago

Dear user, Sorry for the delay. We have now generated and uploaded the files we promised. They have been computed using the Tabula Muris Senis data, so please cite them as well when using these files.

You will find both the mm10 PoN and RNA-editing files in the PoN and RNA-editing folders, respectively.

IMPORTANT: gunzip the files before using them.

Thanks for your patience, Fran

RinconFer commented 9 months ago

Hi, Thank you very much for all the efforts. I have been able to successfully run SComatic in my murine datasets till Step 4.2. In the example tutorial it is suggested to intersect the results from 4.2 with a bed file of high quality regions of the genome. In the tutorial the data is from human and therefore the bed_files_of_interest used is for human data. Is there, to your knowledge, a similar file for mouse data?

Thank you!