Open strohstern opened 11 months ago
The basic vignette for the analysis of PBMC scATAC-seq with Signac (https://stuartlab.org/signac/articles/pbmc_vignette.html#computing-qc-metrics) mentions the fraction of reads in peaks as one of the QC metrics to filter out low quality cells. CellRanger ARC does provide a metadata file that contains the necessary information for that in a file in the outs directory, namely per_barcode_metrics.csv. A more detailed description of the content of this file can be found on the 10X website (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/per_barcode_metrics). The two relevant columns are titled: atac_fragments and atac_peak_region_fragments.
outs
per_barcode_metrics.csv
atac_fragments
atac_peak_region_fragments
It may be good to add this information to the Seurat object during generation.
The basic vignette for the analysis of PBMC scATAC-seq with Signac (https://stuartlab.org/signac/articles/pbmc_vignette.html#computing-qc-metrics) mentions the fraction of reads in peaks as one of the QC metrics to filter out low quality cells. CellRanger ARC does provide a metadata file that contains the necessary information for that in a file in the
outsdirectory, namelyper_barcode_metrics.csv. A more detailed description of the content of this file can be found on the 10X website (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/per_barcode_metrics). The two relevant columns are titled:atac_fragmentsandatac_peak_region_fragments.It may be good to add this information to the Seurat object during generation.