Applications/STAR - Revision history

Pysdlb: /* Usage */

2022-11-17T11:36:50Z

‎Usage

Pysdlb: /* Usage */

2022-11-17T11:34:56Z

‎Usage

Pysdlb: /* Navigation */

2022-11-16T10:59:10Z

‎Navigation

Pysdlb at 13:54, 24 May 2019

2019-05-24T13:54:40Z

Pysdlb at 09:43, 21 November 2018

2018-11-21T09:43:21Z

Pysdlb: Pysdlb moved page STAR to Applications/STAR without leaving a redirect

2017-04-21T10:42:59Z

Pysdlb moved page STAR to Applications/STAR without leaving a redirect

Pysdlb at 10:42, 21 April 2017

2017-04-21T10:42:39Z

Pysdlb: Created page with "TOC ==Application Details== Description: RNA-seq aligner Version: 2016-10-27 Module: STAR/2016-10-27 Licence: Copyrighted by the Regents of the University of Minnes..."

2017-04-21T10:41:59Z

Created page with "__TOC__ ==Application Details== *Description: RNA-seq aligner *Version: 2016-10-27 *Module: STAR/2016-10-27 *Licence: Copyrighted by the Regents of the University of Minnes..."

New page

__TOC__

==Application Details==
*Description: RNA-seq aligner
*Version: 2016-10-27
*Module: STAR/2016-10-27
*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===

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add STAR/2016-10-27
[username@login01 ~]$ STAR --option1-name
</pre>

==Further Information==

* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 23: / Line 23: @@
-===Module===
+===Interactive Session===
 <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@login01 ~]$ module add STAR/2.6.1
-[username@login01 ~]$ STAR --option1-name option1-value(s)--option2-name option2-value(s)
+[username@login01 ~]$ interactive
 </pre>
 ==Further Information==

← Older revision		Revision as of 10:59, 16 November 2022
Line 37:		Line 37:
	* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]		* [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 11: / Line 11: @@
 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.
+* Generating genome index 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.
+* Mapping reads to the genome. In this step, the 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===

@@ Line 4: / Line 4: @@
 *Description:  RNA-seq aligner
 *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.
@@ Line 37: / Line 37: @@
 * [https://github.com/alexdobin/STAR https://github.com/alexdobin/STAR]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

← Older revision	Revision as of 10:42, 21 April 2017
(No difference)

Applications/STAR - Revision history

Pysdlb: /* Usage */

Pysdlb: /* Usage */

Pysdlb: /* Navigation */

Pysdlb at 13:54, 24 May 2019

Pysdlb at 09:43, 21 November 2018

Pysdlb: Pysdlb moved page STAR to Applications/STAR without leaving a redirect

Pysdlb at 10:42, 21 April 2017

Pysdlb: Created page with "__TOC__ ==Application Details== *Description: RNA-seq aligner *Version: 2016-10-27 *Module: STAR/2016-10-27 *Licence: Copyrighted by the Regents of the University of Minnes..."

Pysdlb: Created page with "TOC ==Application Details== Description: RNA-seq aligner Version: 2016-10-27 Module: STAR/2016-10-27 Licence: Copyrighted by the Regents of the University of Minnes..."