Skip to content

read_duplication.py

Calculate reads duplication rate using two methods:

  • Sequence-based: reads with identical sequence are duplicates
  • Mapping-based: reads mapped to the exact same genomic location are duplicates

Usage

read_duplication.py -i input.bam -o output_prefix

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format Required
-o, --out-prefix Prefix of output files Required
-u, --up-limit Upper limit of read occurrence for plotting 500
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.pos.DupRate.xls — position-based duplication rate
  • prefix.seq.DupRate.xls — sequence-based duplication rate
  • prefix.DupRate_plot.r — R script for duplication plot
  • prefix.DupRate_plot.pdf — duplication rate plot (if R is available)