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Application Details

  • Description: RNA-seq aligner
  • Version: 2016-10-27, 2.6.1
  • Module: STAR/2016-10-27 and STAR/2.6.1
  • Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes.


Basic STAR workflow consists of 2 steps:

  • Generating genome indexes files. 2nd (mapping) step. The genome indexes are saved to disk and need only be generated once for each genome/annotation combination.
  • Mapping reads to the genome. In this step user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome, and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, nmapped reads, signal (wiggle) tracks etc.

Command Description

STAR command line has the following format:

STAR --option1-name option1-value(s)--option2-name option2-value(s) ...

If an option can accept multiple values, they are separated by spaces, and in a few cases - by commas.


[username@login01 ~]$ module add STAR/2.6.1
[username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s)

Further Information