Star

Map reads with STAR. Requires the rule to provide named inputs (r1, possibly r2) and a named output (bam), as well as a named param (index).

Software dependencies

• star ==2.6.0c

Example

rule star:
  input:
    fasta = "/path/to/fasta1", "/path/to/fasta2", # Path to the genome fasta file(s).
    gtf = "/path/to/annotations.gtf" # (optional) Path to file with transcript annotations in GTF format.
  output:
    genome = "/path/to/genomeDir", # Path to the directory, where the genome index should be stored.
  params:
    options = "" # Additional command line options.
  wrapper:
    "star"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper star and include it in the snakefile.

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.

Authors

• Johannes Köster
• Jens Preussner