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I am attempting to run a multiomic analysis on some single cell RNA-sequencing data and ATAC-seq data. I have downloaded the scRNA-seq files from GEO in the format of (matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz), and have read them in to R using the Read10X() function. The files are being stored as a Large dgCMatrix. I would appreciate some help figuring out how to go about setting up a Seurat object in an appropriate way using the dgCMatrix, such that I can then use the "CreateChromatinAssay" function to add the "ATAC" assay to it as well as the path to the fragment file.

How can I go about structuring the data I am importing in the .tsv format such that it is appropriate for Seurat, as it is not provided in the .h5 object format with "counts" readily available?

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Apr 18 at 21:32
  • $\begingroup$ We can't really help you with data that you don't show. Please edit your question and add a few lines of your input files so we can understand their format, and then also show us the R code you used to read them. Ideally, show us the expected output format (what Seurat wants) as well, but if that is actually what you want from us, just edit to clarify that this is what you're asking (I can't tell if you know what the format is but need help to get your data in that format or if you don't know the format at all). $\endgroup$
    – terdon
    Apr 18 at 23:32
  • $\begingroup$ Please let us know what you've already attempted, especially if you've been following any of Seurat's integration tutorials. $\endgroup$
    – gringer
    Apr 21 at 4:42

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Given that you've mentioned Seurat, have you looked at the scATAC-seq integration tutorial?

https://satijalab.org/seurat/articles/seurat5_atacseq_integration_vignette

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