Difference between revisions of "Applications/STAR"
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*Description: RNA-seq aligner | *Description: RNA-seq aligner | ||
*Version: 2016-10-27, 2.6.1 | *Version: 2016-10-27, 2.6.1 | ||
| − | *Module: STAR/2016-10-27 and /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. | *Licence: Copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes. | ||
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* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR] | * [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR] | ||
| − | + | ==Navigation== | |
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* [[Main_Page|Home]] | * [[Main_Page|Home]] | ||
| − | * [[Applications|Application support]] | + | * [[Applications|Application support]] * |
* [[General|General]] | * [[General|General]] | ||
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* [[Programming|Programming support]] | * [[Programming|Programming support]] | ||
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Revision as of 13:54, 24 May 2019
Contents
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.
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)