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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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How to process cellranger-atac count output for scATAC-seq data integration vignette? #190

Closed singcell closed 4 years ago

singcell commented 4 years ago

I am comparing control and treated samples using Signac data integration vignette. However in the tutorial you use "Cell metadata" and "Count matrix" which is already processed data. I have raw scATAC-seq output from cellranger-atac count and wanted to perform integration. I was wondering how to process cellranger-atac count raw data to get "Cell metadata" and "Count matrix" so that I can use it with Signac.

Thank you

timoast commented 4 years ago

I was wondering how to process cellranger-atac count raw data to get "Cell metadata" and "Count matrix" so that I can use it with Signac.

The cell metadata and count matrix files are outputs of cellranger-atac, and are used as input for most of the Signac vignettes.