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nghiavtr / SCmut

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Can SCmut be used in 10x genomics single cell rnaseq data? #7

Open mawusseAgbessi opened 2 years ago

mawusseAgbessi commented 2 years ago

Hi,

Thank a lot for this tools. I have some 10x genomics scRNA-seq 3'data. So I have one bam file per sample , with barcoded reads represented each cell. I was wondering if I can use this tools on this type of data.

Also, a well known usage of 10X is the clustering in cell types. Is possible to use scMut on a cluster?

Thanks you !

nghiavtr commented 2 years ago

Hi @mawusseAgbessi,

Thank you for using scMut in your research.

Technically, you can apply the method as long as the basic inputs including raFull, rrFull, mut.sites to run function scfdr() are ready, please see the example in https://github.com/nghiavtr/SCmut#5-cell-level-mutation-detection.

I also think applying scMut to a cell cluster of interest is fine, it depends on your scientific question. The collection of cells in a cluster can be used for randomization to build statistics of null variants for computing fdr2d.

Actually, we do not have experience in running scMut for 10x data which has low coverage and a high number of cells. From our previous experience with SmartSeq data, mutations generally can be detected better with high coverage samples. However if your mutations of interest belong to highly expressed genes in 10x data, you still can get strong signals.

Best, Nghia

jgarces02 commented 1 year ago

Hi @mawusseAgbessi. Have any feedback about applying this method to your 10X 3' data?