isoseq 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
This tool should be run after
# Example: isoseq bcstats --json sample.bcstats.json -o sample.bcstats.tsv corrected.bam
--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”).
By default, the program only emits stats on group barcodes. Adding
--umi will cause stats for the full molecular barcodes to be emitted as well.
Note that, if
isoseq correct was called using the percentile method (see Cell Calling), then
isoseq bcstats need to use the same parameters as well. For example:
isoseq correct --method percentile --percentile 90 ... isoseq bcstats --method percentile --percentile 90