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read_NVC.py

Check nucleotide frequency at each position of the read (5' to 3'). Generates a Nucleotide Versus Cycle (NVC) plot.

Usage

read_NVC.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
-x, --nx Include N and X nucleotides in the NVC plot Off
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.NVC.xls — tab-separated nucleotide frequencies per position
  • prefix.NVC_plot.r — R script for NVC plot
  • prefix.NVC_plot.pdf — NVC plot (if R is available)