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rQuant | Transcript quantification with RNA-Seq data

Infers the abundance of given transcripts from RNA-Seq data. rQuant is a method based on solving quadratic programming problems. The software achieves the highest accuracy when estimating density biases and considering the read coverages at each nucleotide independently. The web service Quant.web facilitates an easy interaction between integrated tools, stores the queries and results in user histories, and conveniently uses workflows for re-occurring tasks.

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rQuant classification

rQuant specifications

Unique identifier:
OMICS_01286
Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Stability:
Stable
Alternative name:
rQuant.web
Interface:
Command line interface
Operating system:
Unix/Linux
Version:
2.1
Maintained:
Yes

rQuant distribution

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rQuant classification

rQuant specifications

Unique identifier:
OMICS_01286
Interface:
Web user interface
Input data:
The annotation file containing the necessary information about the transcripts that are to be quantified and the alignment file, which stores the read alignments in a compressed format.
Output data:
A file with the attributes ARC and RPKM that describe the abundance of a transcript in ARC (estimated average read coverage) and RPKM (reads per kilobase of exon model per million mapped reads), respectively.
Computer skills:
Basic
Maintained:
Yes
Alternative name:
rQuant.web
Restrictions to use:
None
Input format:
GFF, BAM
Output format:
GFF3
Stability:
Stable

rQuant support

Maintainers

  • Gunnar Rätsch <>
  • Regi Bohnert <>
  • Regina Bohnert <>
  • Gunnar Rätsch <>
  • Regi Bohnert <>
  • Regina Bohnert <>

Additional information

Web app: https://galaxy.inf.ethz.ch/

Credits

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Publications

Institution(s)

Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany

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