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shortran: A pipeline for small RNA-seq data analysis

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shortran : A pipeline for small RNA-seq data analysis. / Gupta, Vikas; Markmann, Katharina; Pedersen, Christian Nørgaard Storm; Stougaard, Jens; Andersen, Stig Uggerhøj.

I: Bioinformatics, Bind 28, Nr. 20, 2012, s. 2698-2700.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Gupta, Vikas ; Markmann, Katharina ; Pedersen, Christian Nørgaard Storm ; Stougaard, Jens ; Andersen, Stig Uggerhøj. / shortran : A pipeline for small RNA-seq data analysis. I: Bioinformatics. 2012 ; Bind 28, Nr. 20. s. 2698-2700.

Bibtex

@article{444dc746c5f242308a6107a8129dcdf2,
title = "shortran: A pipeline for small RNA-seq data analysis",
abstract = "SUMMARY: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data-sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation, and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output. AVAILABILITY: shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/Contacts: vgupta@cs.au.dk, sua@mb.au.dk SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.",
author = "Vikas Gupta and Katharina Markmann and Pedersen, {Christian N{\o}rgaard Storm} and Jens Stougaard and Andersen, {Stig Uggerh{\o}j}",
year = "2012",
doi = "10.1093/bioinformatics/bts496",
language = "English",
volume = "28",
pages = "2698--2700",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "20",

}

RIS

TY - JOUR

T1 - shortran

T2 - A pipeline for small RNA-seq data analysis

AU - Gupta, Vikas

AU - Markmann, Katharina

AU - Pedersen, Christian Nørgaard Storm

AU - Stougaard, Jens

AU - Andersen, Stig Uggerhøj

PY - 2012

Y1 - 2012

N2 - SUMMARY: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data-sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation, and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output. AVAILABILITY: shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/Contacts: vgupta@cs.au.dk, sua@mb.au.dk SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

AB - SUMMARY: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data-sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation, and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output. AVAILABILITY: shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/Contacts: vgupta@cs.au.dk, sua@mb.au.dk SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

U2 - 10.1093/bioinformatics/bts496

DO - 10.1093/bioinformatics/bts496

M3 - Journal article

C2 - 22914220

VL - 28

SP - 2698

EP - 2700

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 20

ER -