READ_DISTRIBUTION

calculate how mapped reads were distributed over genome feature

URL: https://rseqc.sourceforge.net/#read-distribution-py

Example

This wrapper can be used in the following way:

rule test_rseqc_read_distribution:
    input:
        aln="A.bam",
        refgene="annotation.bed",
    output:
        "a.read_distribution.txt",
    log:
        "rseqc.log",
    wrapper:
        "v3.9.0/bio/rseqc/read_distribution"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• rseqc=5.0.3

Input/Output

Input:

• aln: Path to SAM/BAM input file

• refgene: Path to refgene model (BED)

Output:

• Path to read distribution (txt)

Authors

• Thibault Dayris

Code

# coding: utf-8

__author__ = "Thibault Dayris"
__mail__ = "thibault.dayris@gustaveroussy.fr"
__copyright__ = "Copyright 2024, Thibault Dayris"
__license__ = "MIT"

from snakemake import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell(
    "read_distribution.py "
    "--input-file {snakemake.input.aln} "
    "--refgene {snakemake.input.refgene} "
    "> {snakemake.output} {log} "
)