shortran: A pipeline for small RNA-seq data analysis

Vikas Gupta; Katharina Markmann; Christian Nørgaard Storm Pedersen; Jens Stougaard; Stig Uggerhøj Andersen

doi:10.1093/bioinformatics/bts496

shortran: A pipeline for small RNA-seq data analysis

Vikas Gupta, Katharina Markmann, Christian Nørgaard Storm Pedersen, Jens Stougaard, Stig Uggerhøj Andersen

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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: [email protected], [email protected] SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

Original language	English
Journal	Bioinformatics
Volume	28
Issue	20
Pages (from-to)	2698-2700
Number of pages	2
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/bts496
Publication status	Published - 2012

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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: [email protected], [email protected] SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.",

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T2 - A pipeline for small RNA-seq data analysis

AU - Gupta, Vikas

AU - Markmann, Katharina

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AU - Andersen, Stig Uggerhøj

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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: [email protected], [email protected] 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: [email protected], [email protected] SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

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shortran: A pipeline for small RNA-seq data analysis

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