Difference between revisions of "RSeQC"

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

Latest revision as of 14:18, 23 February 2017

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>