sc_bamStat.py¶
Report single-cell RNA-seq (scRNA-seq) mapping statistics from a BAM file generated by the Cell Ranger workflow.
Usage¶
Options¶
| Option | Description | Default |
|---|---|---|
-i, --infile | Input BAM file with Cell Ranger alignment tags | Required |
--cb-tag | BAM tag for error-corrected cellular barcode | CB |
--re-tag | BAM tag for region type (E=exonic, N=intronic, I=intergenic) | RE |
--tx-tag | BAM tag for sense-strand transcript alignment | TX |
--an-tag | BAM tag for antisense-strand transcript alignment | AN |
--umi-tag | BAM tag for error-corrected UMI | UB |
--xf-tag | BAM tag for confidently mapped reads | xf |
--chrM-id | Name of the mitochondrial chromosome | chrM |
--verbose | Print detailed running information | Off |
Output¶
Summary statistics for the single-cell BAM file, including per-cell barcode counts and mapping categories.