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pachterlab / monod

The Monod package fits CME models to sequencing data.
BSD 2-Clause "Simplified" License
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10X multiome #14

Open jsacco1 opened 9 months ago

jsacco1 commented 9 months ago

Hello, I am interested in the application of this tool to 10X multiome data. I have the following output files from CellRanger: atac_fragments.tsv.gz atac_fragments.tsv.gz.tbi filtered_feature_bc_matrix.h5 per_barcode_metrics.csv summary.csv web_summary.html

How could I get Monod to process this? Thanks

gennadygorin commented 9 months ago

Thank you very much for your interest in Monod! To use the package with spliced/unspliced data, you will want to create a loom file with spliced/unspliced layers. The scanpy and loom packages have this functionality. As a caveat, Monod has mostly been tested with kb and velocyto outputs, so performance will be better if alignment is consistent with their rules.

Monod does not currently support ATAC data. The precise physical relationship between RNA and ATAC readouts, as well as the noise behaviors in the latter, are still obscure. Developing such a multiomic model is an active area of research in the laboratory. I expect, however, that this could work even without a model, by correlating ATAC to inferred parameters.

jsacco1 commented 9 months ago

Thank you so much for the quick response. I will try out your suggested methods for input. All the best, and I look forward to seeing how Monod evolves.