RSeQC

Introduction

This is a python package (so no special module loading is required) and is especially used for its inner_distance.py and geneBody_coverage.py scripts.

Usage

inner_distance.py -i <bamfile> -r <reference_rendered_as_gene_model_bed_file> -o <output_dir>

This should give a PDF plot.

geneBody_coverage.py -i <bamfile> -r <reference_rendered_as_gene_model_bed_file> -o <output_dir>

Also:

junction_annotation.py -i <bamfile> -r <reference_rendered_as_gene_model_bed_file> -o <output_dir>

junction_saturation.py -i <bamfile> -r <reference_rendered_as_gene_model_bed_file> -o <output_dir>