.. _`star`:

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
-------

.. code-block:: bash

  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

.. code-block:: bash

  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

.. code-block:: bash

    snakemake --use-conda

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




Authors
-------


* Johannes Köster

* Jens Preussner