Difference between revisions of "RSeQC"
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= Introduction = | = Introduction = | ||
| − | This is a python package (so no special module loading is required) and is especially used for its '''inner_distance.py''' | + | 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 = | = Usage = | ||
inner_distance.py -i <bamfile> -r <reference_rendered_as_gene_model_bed_file> -o <output_dir> | 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> | ||
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>
