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geneBody_coverage.py

Calculate RNA-seq read coverage over the gene body. This is useful for assessing RNA integrity and 3'/5' bias.

Note

  • Only sorted and indexed BAM files are supported (not SAM)
  • Genes/transcripts with mRNA length < 100 bp are skipped

Usage

geneBody_coverage.py -i input.bam -r gene_model.bed -o output_prefix

Options

Option Description Default
-i, --input Input BAM file(s). Accepts a single BAM, comma-separated BAMs, or a text file listing BAM paths Required
-r, --refgene Reference gene model in BED format Required
-o, --out-prefix Prefix of output files Required
-l, --minimum_length Minimum mRNA length (bp) 100
-f, --format Output figure format: pdf, png, or jpeg pdf

Output

  • prefix.geneBodyCoverage.curves.pdf — gene body coverage plot
  • prefix.geneBodyCoverage.txt — coverage percentiles (0–100)
  • prefix.geneBodyCoverage.r — R script for coverage plot