Applications/Trinityrnaseq - Revision history

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Pysdlb at 09:38, 19 April 2017

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Pysdlb: Created page with "TOC ==Application Details== * Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. * Version: 2.2.0 (compiled with 2.2.0) * Modules: trinityrn..."

2017-04-19T09:38:16Z

Created page with "__TOC__ ==Application Details== * Description: Trinity assembles transcript sequences from Illumina RNA-Seq data. * Version: 2.2.0 (compiled with 2.2.0) * Modules: trinityrn..."

New page

__TOC__

==Application Details==

* Description: Trinity assembles transcript sequences from Illumina RNA-Seq data.
* Version: 2.2.0 (compiled with 2.2.0)
* Modules: trinityrnaseq/gcc/2.2.0
* Licence: Github, open-source

==Usage==

This 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 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.

===Assemble a small synthetic data set===

Assemble RNA-Seq data like so:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

[username@login] module add trinityrnaseq/gcc/2.2.0
[username@login] Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G

</pre>

Find assembled transcripts as: 'trinity_out_dir/Trinity.fasta'

A typical script would be:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
#!/bin/bash

if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
gunzip -c reads2.left.fq.gz > reads2.left.fq
fi

#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup --normalize_reads

##### Done Running Trinity #####

if [ ! $* ]; then
exit 0
fi

</pre>

===Parallel processing===

'''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3
[username@c230 ~]$ mpirun abyss-pe np=40

</pre>

==Further Information==

* [https://github.com/trinityrnaseq/trinityrnaseq/wiki https://github.com/trinityrnaseq/trinityrnaseq/wiki]

{|
|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 11:00, 16 November 2022
Line 71:		Line 71:
	* [https://github.com/trinityrnaseq/trinityrnaseq/wiki https://github.com/trinityrnaseq/trinityrnaseq/wiki]		* [https://github.com/trinityrnaseq/trinityrnaseq/wiki https://github.com/trinityrnaseq/trinityrnaseq/wiki]

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

← Older revision		Revision as of 09:39, 19 April 2017
Line 19:		Line 19:


−	===Assemble ~~a small synthetic~~ data ~~set~~===	+	===Assemble RNA-Seq data===
−
−	~~Assemble RNA-Seq data like so:~~

	<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">		<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

← Older revision		Revision as of 09:38, 19 April 2017
Line 68:		Line 68:


−
−	~~===Parallel processing===~~
−
−
−	~~'''Note''': this example is done on a high memory node, usually access would be achieved with the scheduler~~
−
−	~~<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">~~
−
−	~~[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3~~
−	~~[username@c230 ~]$ mpirun abyss-pe np=40~~
−
−	~~</pre>~~

@@ Line 10: / Line 10: @@
 ==Usage==
-This 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 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:
+This 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 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.
+* Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptional 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.
+* Butterfly then processes the individual graphs in parallel, tracing the paths that read and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that correspond to paralogous genes.

@@ Line 71: / Line 71: @@
 * [https://github.com/trinityrnaseq/trinityrnaseq/wiki https://github.com/trinityrnaseq/trinityrnaseq/wiki]
-{|
+==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]]

@@ Line 4: / Line 4: @@
 * Description: Trinity assembles transcript sequences from Illumina RNA-Seq data.
-* Version: 2.2.0 (compiled with 2.2.0)
+* Version: 2.2.0, 2.5.1 and 2.8.2
-* Modules: trinityrnaseq/gcc/2.2.0
+* Modules: trinityrnaseq/gcc/2.2.0, /2.5.1 and /2.8.2
 * Licence: Github, open-source
@@ Line 23: / Line 23: @@
 <pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
-[username@login] module add trinityrnaseq/gcc/2.2.0
+[username@login] module add trinityrnaseq/gcc/2.8.2
 [username@login] Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G
@@ Line 64: / Line 64: @@
 </pre>

← Older revision	Revision as of 09:40, 19 April 2017
(No difference)