RNA-SeQC Python utilities

This module contains utility code for RNA-SeQC

Installing

• From pip: pip install rnaseqc
• From the git repo: pip install -e python (Invoke from root of git repo)

Usage

This does not install a console entrypoint. You can invoke the utilities in one of three ways:

• From the main module: python3 -m rnaseqc ...
• Calling the target module: python3 -m rnaseqc.example ...
• Calling scripts directly: python3 python/rnaseqc/example.py

Utilities

The rnaseqc module contains 5 main utilities. To get more help with each utility, invoke the utility with the -h or --help option

Aggregation

Aggregates RNA-SeQC outputs from multiple samples

python3 -m rnaseqc aggregate [-h] [--parquet] [-o OUTPUT_DIR] results_dir prefix

Jupyter Notebooks

Creates a jupyter notebook with several figures for comparing samples

python3 -m rnaseqc notebook [-h] [-t TPM] [-i INSERT_SIZE] [-c COHORT] [-d DATE] metrics output

Figures

Generates figures from an aggregated RNA-SeQC metrics table

python3 -m rnaseqc report [-h] [--tpm TPM] [--insert-size INSERT_SIZE] [--cohort COHORT] [--output-dir OUTPUT_DIR] [--dpi DPI] metrics prefix

Insert Size distributions

Generates a BED file with intervals used by RNA-SeQC for estimating a sample's insert size distribution

python3 -m rnaseqc insert-size [-h] [--min-length MIN_LENGTH] [--min-mappability MIN_MAPPABILITY] [--output-dir OUTPUT_DIR] gtf_path mappability_bigwig prefix

Exon remapping

Convert exon names in an *.exon_reads.gct file from RNA-SeQC 2.X.X to match names as reported by RNA-SeQC 1.1.9

python3 -m rnaseqc legacy-exons gct gtf