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RPKM_saturation.py

Assess whether RPKM values are saturated by re-sampling reads at increasing percentages. Strand-specific protocols are supported.

Usage

RPKM_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
-d, --strand Strand rule: 1++,1--,2+-,2-+ or 1+-,1-+,2++,2-- or none None
-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
-c, --rpkm-cutoff Ignore transcripts with RPKM below this value 0.01
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.saturation.r — R script for saturation plot
  • prefix.saturation.pdf — saturation plot (if R is available)
  • prefix.rawCount.xls — raw count at each sampling level
  • prefix.eRPKM.xls — estimated RPKM values