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The FLUX CAPACITOR | Transcriptome genetics using second generation sequencing in a Caucasian population

Allows users to simulate RNA-Seq experiments in silico. The FLUX CAPACITOR is a pipeline that consists of flexible modules to determine abundance and distribution of read tags according to user-desired experimental protocol, including arbitrary protocols. It also provides an assortment of optional steps for modeling the final library preparation, comprising in silico ligation of adapter sequences and polymerase chain reaction (PCR) amplification.

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The FLUX CAPACITOR forum

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The FLUX CAPACITOR classification

The FLUX CAPACITOR specifications

Unique identifier:
OMICS_01293
Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTA+GTF
Output format:
SAM
Programming languages:
Java
Version:
1.6.1
Maintained:
Yes
Alternative name:
Flux Simulator
Interface:
Command line interface
Input data:
An annotation of a reference transcriptome and reads fromRNAseq technologies aligned to the genome.
Output data:
Some reads and mappings
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

The FLUX CAPACITOR distribution

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The FLUX CAPACITOR support

Documentation

Maintainer

  • Michael Sammeth <>

Credits

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Publications

Institution(s)

Bioinformatics and Genomics Program, Centre de Regulacio Genomica (CRG), Barcelona, Spain; Functional Bioinformatics Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona; Computational Biology and Regulatory Networks Group, Gene Center Munich, Munich, Germany; Algorithm Development Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona, Spain; Statistical Genomics Group, Centre Nacional d’Analisi Genomica (CNAG), Barcelona, Spain; Biometrie et Biologie Evolutive, Universite Lyon 1, Villeurbanne, France

Funding source(s)

Supported by the European Science Foundation, an Erasmus exchange grant of the European Community, a Post-doctoral fellowship of the Spanish Ministry of Science and Open Source license of Atlassian for their products Jira, Confluence and Fisheye and the Spanish Ministry of Science [BIO2006-03380 and CONSOLIDER CSD2007-00050].

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