Sequgio pipeline

Sequgio specifications

Information


Unique identifier OMICS_01290
Name Sequgio
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yudi Pawitan <>

Publication for Sequgio

Sequgio IN pipelines

 (2)
2016
PMCID: 5356595
PMID: 27634900
DOI: 10.18632/oncotarget.11998

[…] reads were generated per sample. reads were mapped to human hg19 ucsc annotation reference using tophat [45] and bowtie [46] to create the bam files., isoform-level expression is estimated using sequgio analysis pipeline [44] (following the instruction of its webpage http://fafner.meb.ki.se/biostatwiki/sequgio/), which reports expression values in units of fragments per kilobase […]

2016
PMCID: 5356595
PMID: 27634900
DOI: 10.18632/oncotarget.11998

[…] and bowtie [46] to create the bam files., isoform-level expression is estimated using sequgio analysis pipeline [44] (following the instruction of its webpage http://fafner.meb.ki.se/biostatwiki/sequgio/), which reports expression values in units of fragments per kilobase of transcript per million mapped reads (fpkm). gene-level fpkm is defined as the sum of the isoform-level expression. […]

Sequgio institution(s)
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Molecular and Translational Medicine, University of Brescia, Italy; Department of Mathematics and Statistics, La Trobe University, Melbourne, VIC, Australia
Sequgio funding source(s)
Supported by Swedish Research Council (in part) 621-2009-5900.

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