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| == Introduction == | | == Introduction == |
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| 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 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:
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| *'''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.
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| *'''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.
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| *'''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.
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| == Installed version == | | == Installed version == |
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| There are currently two version of Trinity installed:
| | Currently there is one version installed: |
| | On '''hpc-env/6.4''' |
| | *'''Theano/1.0.1-foss-2017b-Python-3.6.3''' |
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| '''hpc-uniol-env'''
| | == Using Theano == |
| *'''2.2.0'''
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| *'''2.4.0'''
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| '''hpc-env/6.4'''
| | To use Theano, at first you have to load the corresponding module. |
| *'''2.6.6-intel-2018a'''
| | module load hpc-env/6.4 |
| | module load Theano |
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| == Using Trinity ==
| | Afterwards, you have to start ''Python'' and import Theano: |
| | | python |
| To use Trinity, you just have to load the corresponding module.
| | from theano import * |
| For the newest version, 2.6.6 that is, you have to change the environment first.
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| module load hpc-env/6.4 | |
| module load 2.6.6-intel-2018a | |
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| == Documentation == | | == Documentation == |
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| The full documentation can be found [https://github.com/trinityrnaseq/trinityrnaseq/wiki here]. | | The full documentation can be found [http://deeplearning.net/software/theano/index.html here]. |
| | To learn how to use Theanos, you could also take a look at the [http://deeplearning.net/software/theano/tutorial/index.html tutorial]. |
Revision as of 09:19, 7 November 2018
Introduction
Installed version
Currently there is one version installed:
On hpc-env/6.4
- Theano/1.0.1-foss-2017b-Python-3.6.3
Using Theano
To use Theano, at first you have to load the corresponding module.
module load hpc-env/6.4
module load Theano
Afterwards, you have to start Python and import Theano:
python
from theano import *
Documentation
The full documentation can be found here.
To learn how to use Theanos, you could also take a look at the tutorial.
