Barcode Statistics Documentation

isoseq bcstats emits statistics for each barcode:

  1. Barcode sequence
  2. Number of reads matching the barcode
  3. Frequency Rank (within barcodes)
  4. Number of unique molecular barcodes matching this barcode
  5. Whether the barcode is Group/Cell barcode or a Molecular Barcode/UMI

This tool should be run after isoseq correct.

# Example:
isoseq bcstats --json sample.bcstats.json -o sample.bcstats.tsv corrected.bam

If --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

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