Applications/Wgs - Revision history

Pysdlb at 13:45, 24 May 2019

2019-05-24T13:45:40Z

Pysdlb at 09:31, 25 April 2017

2017-04-25T09:31:20Z

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

2017-04-25T08:42:48Z

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

Pysdlb at 08:42, 25 April 2017

2017-04-25T08:42:11Z

Pysdlb: Created page with "TOC ==Application Details== Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2..."

2017-04-25T08:41:19Z

Created page with "__TOC__ ==Application Details== *Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. *Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2..."

New page

__TOC__
==Application Details==
*Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.
*Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2
*Module: bridger/r2014-12-01, bridger/r2014-12-01.1, and bridger/r2014-12-01.2
*Licence: SourceForge, open source

==Usage Examples==

Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference. The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first, Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes.

Then, Bridger uses a rigorous mathematical model called minimum path cover to search minimal set of paths(transcripts) that can be supported by our data and could explain all observed splicing events of each locus.

===Module===

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module add wgs/8.3rc2
[username@login01 ~]$ fragmentDepth MODE -min 64 -max 1024 -stepSize 2 < x.posmap.frgscf
</pre>

==Further Information==

* [http://wgs-assembler.sourceforge.net/wiki/index.php http://wgs-assembler.sourceforge.net/wiki/index.php]

{|
|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]]
|-
|}

← Older revision		Revision as of 09:31, 25 April 2017
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	Then, Bridger uses a rigorous mathematical model called minimum path cover to search minimal set of paths(transcripts) that can be supported by our data and could explain all observed splicing events of each locus.		Then, Bridger uses a rigorous mathematical model called minimum path cover to search minimal set of paths(transcripts) that can be supported by our data and could explain all observed splicing events of each locus.
		+
		+	'''Note''' : Celera Assembler is no longer being maintained by the developers

	===Module===		===Module===

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 * [http://wgs-assembler.sourceforge.net/wiki/index.php http://wgs-assembler.sourceforge.net/wiki/index.php]
-{|
+==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 08:42, 25 April 2017
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