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Iso-Seq Docs

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

This tool should be run after isoseq3 correct.

# Example:
isoseq3 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 isoseq3 correct was called using the percentile method (see Cell Calling), then isoseq3 bcstats need to use the same parameters as well. For example:

isoseq3 correct --method percentile --percentile 90 ...
isoseq3 bcstats --method percentile --percentile 90

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