Skip to content
No description, website, or topics provided.
Python
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
LICENSE
README.md
correct_barcode.py

README.md

correct_bacode.py

DOI

The command corrects a DNA sequencing error of cell barcoding containing RT primer sets for Quartz-Seq2 which one of a high throughput single-cell RNA-sequencing [1]. The cell barcodes of Quartz-Seq2 are designed such that the minimum Sequence–Levenshtein distance between two sequences should be greater than 5, which leads to the correction of two nucleotides of mismatch, insertion, and deletion in sequence reads [2]. The program can correct cell barcode if sequence error occurs.

  1. Sasagawa Y et al. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
  2. Buschmann T. DNABarcodes: an R package for the systematic construction of DNA sample tags. Bioinformatics. 2017;:btw759.

Requirements

  • R
  • Python 2.7
    • numpy==1.11.0
    • pandas==0.18.0
    • pyper==1.1.2
    • pysam==0.9.0
    • seaborn==0.7.0

Usage

correct_barcode.py

Usage:
    correct_barcode.py (-i input_file) (-b barcode_file) (-o output_file) (-m metric) (-d distance)
    correct_barcode.py -h | --help
    correct_barcode.py -v | --version

Options:
    -i input_file       Bam file resulted of TagReadWithGeneExon
    -b barcode_file     Single-column file for designed barcode (No header)
    -o output_file      Bam file name for output of this program
    -m metric           The distance metric to be used. (seqlev or hamming)
    -d distance         Distance for error correction
    -h --help           Show this screen
    -v --version        Show version

Lisense

MIT

You can’t perform that action at this time.