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Barcode Statistics Documentation

isoseq3 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

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”).

# Example:
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.

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