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:
    r1 = "fastq/{sample}_R1.fastq", # Path to the first fastq file, in case of paired-end sequencing the first mate. Can be a list of files.
    r2 = "fastq/{sample}_R2.fastq" # (optional) Path to the second fastq file. Can be a list of files as well.
  output:
    genome_bam = "mapped/{sample}.bam", # Path to the genome alignment file.
    transcriptome_bam = "mapped/{sample}.transcriptome.bam" # (optional) Path to the transcriptome alignment file.
  params:
    index = "index/" # Path to the genome index.
    gtf = "/path/to/annotation.gtf" # (optional) Path to a GTF annotation file that sould be used on the fly.
    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