Trinity r20131110 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T14:45:16Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:45, 15 June 2023
Line 12:		Line 12:
	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## Trinity r20131110 modulefile		## Trinity r20131110 modulefile
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	prepend-path PATH $trinity_r20131110_root		prepend-path PATH $trinity_r20131110_root

	</~~source~~>		</pre>

	== Installation details ==		== Installation details ==
Line 36:		Line 36:
	http://sourceforge.net/projects/trinityrnaseq/files/		http://sourceforge.net/projects/trinityrnaseq/files/
	Building of Inchworm and Chrysalis was done by simply issuing:		Building of Inchworm and Chrysalis was done by simply issuing:
	<~~source lang='bash'~~>		<pre>
	make		make
	</~~source~~>		</pre>

Megen002: /* Module file */

2014-03-16T10:40:06Z

Module file

← Older revision		Revision as of 12:40, 16 March 2014
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	module-whatis "Adds Trinity r20131110 to your environment"		module-whatis "Adds Trinity r20131110 to your environment"

			module load bowtie/1-1.0.0

	set trinity_r20131110_root /cm/shared/apps/SHARED/Trinity/trinityrnaseq_r20131110/		set trinity_r20131110_root /cm/shared/apps/SHARED/Trinity/trinityrnaseq_r20131110/

	prepend-path PATH $trinity_r20131110_root		prepend-path PATH $trinity_r20131110_root


	</source>		</source>

Megen002: Created page with "'''[http://trinityrnaseq.sourceforge.net/#running_trinity Trinity]''', developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for t..."

2014-03-15T22:04:42Z

Created page with "'''[http://trinityrnaseq.sourceforge.net/#running_trinity Trinity]''', developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for t..."

New page

'''[http://trinityrnaseq.sourceforge.net/#running_trinity Trinity]''', developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

* Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

* Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.

* Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.

== Module file ==
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/

<source lang='tcl'>
#%Module1.0#######################################################################
## Trinity r20131110 modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds Trinity r20131110 to your environment"
}

module-whatis "Adds Trinity r20131110 to your environment"

set trinity_r20131110_root /cm/shared/apps/SHARED/Trinity/trinityrnaseq_r20131110/

prepend-path PATH $trinity_r20131110_root

</source>

== Installation details ==

The source was downloaded from SourceForge on 15-03-2014:
http://sourceforge.net/projects/trinityrnaseq/files/
Building of Inchworm and Chrysalis was done by simply issuing:
<source lang='bash'>
make
</source>

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://trinityrnaseq.sourceforge.net/#running_trinity Trinity home page]
* [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology paper on Trinity]