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junction_saturation.py

Assess whether sequencing depth is sufficient for junction discovery. As sequencing depth approaches saturation, fewer new junctions are discovered.

Usage

junction_saturation.py -i input.bam -r gene_model.bed -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
-r, --refgene Reference gene model in BED format Required
-l, --percentile-floor Sampling starts from this percentile 5
-u, --percentile-ceiling Sampling ends at this percentile 100
-s, --percentile-step Sampling step size 5
-m, --min-intron Minimum intron size (bp) 50
-v, --min-coverage Minimum supporting reads to call a junction 1
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.junctionSaturation_plot.r — R script for saturation plot
  • prefix.junctionSaturation_plot.pdf — saturation curve (known, novel, all junctions)