Barcode Statistics Documentation
isoseq3 bcstats emits statistics for each barcode:
- Barcode sequence
- Number of reads matching the barcode
- Frequency Rank (within barcodes)
- Number of unique molecular barcodes matching this barcode
- Whether the barcode is Group/Cell barcode or a Molecular Barcode/UMI
--json is unset, JSON summary information is written to stderr (“/dev/stderr”). Similarly, if ‘-o’ is unset, output TSV information is written to stdout (“/dev/stdout”).
isoseq3 bcstats --json sample.bcstats.json -o sample.bcstats.tsv sample.bam
In default behavior, the program only emits stats on group barcodes. Adding
--umi will cause stats for the full molecular barcodes to be emitted as well.