Difference between revisions of "Applications/STAR"
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==Application Details== | ==Application Details== | ||
*Description: RNA-seq aligner | *Description: RNA-seq aligner | ||
| − | *Version: 2016-10-27 | + | *Version: 2016-10-27, 2.6.1 |
| − | *Module: STAR/2016-10-27 | + | *Module: STAR/2016-10-27 and /2.6.1 |
*Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes. | *Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes. | ||
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<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module add STAR/ | + | [username@login01 ~]$ module add STAR/2.6.1 |
[username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s) | [username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s) | ||
</pre> | </pre> | ||
Revision as of 09:43, 21 November 2018
Application Details
- Description: RNA-seq aligner
- Version: 2016-10-27, 2.6.1
- Module: STAR/2016-10-27 and /2.6.1
- Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes.
Usage
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.
Module
[username@login01 ~]$ module add STAR/2.6.1 [username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s)
Further Information
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