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rQuant specifications

Information


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

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Maintainers


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

Additional information


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

Information


Unique identifier OMICS_01286
Name rQuant
Alternative name rQuant.web
Interface Web user interface
Restrictions to use None
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.
Input format GFF, BAM
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.
Output format GFF3
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


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

Additional information


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

Publications for rQuant

rQuant in publications

 (2)
PMCID: 3851240
PMID: 24185837
DOI: 10.1038/nmeth.2714

[…] the transcript assembly process and may be useful in refining the coordinates of exon and transcript boundaries. where a finished genome and high-quality annotation are available, cufflinks and rquant (part of the mgene protocol) can be applied solely for transcript quantification, which can be further improved by correcting for fragment bias. gene prediction algorithms such as augustus […]

PMCID: 3757060
PMID: 24009496
DOI: 10.1371/journal.pcbi.1003210

[…] os cells were determined using ebayes ., microrna expression data were annotated with mirbase release 18 , background corrected by normexp+offset 10 , and normalized with printtiploess followed by rquant . in the differential expression analysis we considered the top 75% of microrna probes that showed largest variation over all samples. multiple test correction was performed using benjamini […]


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rQuant institution(s)
Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany

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