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10X multiome #14

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jsacco1 opened this issue Nov 20, 2023 · 2 comments
Open

10X multiome #14

jsacco1 opened this issue Nov 20, 2023 · 2 comments

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@jsacco1
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jsacco1 commented Nov 20, 2023

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
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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
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jsacco1 commented Nov 22, 2023

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.

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