Link Search Menu Expand Document

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.


THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.