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geneBody_coverage2.py

Calculate RNA-seq read coverage over the gene body using a BigWig file as input (instead of BAM).

Usage

geneBody_coverage2.py -i input.bw -r gene_model.bed -o output_prefix

Options

Option Description Default
-i, --input-file Coverage signal file in BigWig format Required
-r, --refgene Reference gene model in BED format Required
-o, --out-prefix Prefix of output files Required
-t, --graph-type Output format: pdf, jpeg, bmp, tiff, or png pdf

Output

  • prefix.geneBodyCoverage.curves.pdf — gene body coverage plot
  • prefix.geneBodyCoverage.txt — coverage percentiles