shortran: a pipeline for small RNA-seq data analysis.
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.


BACKGROUND
shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/.
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark. vgupta@cs.au.dk
Vikas
V
Gupta
Katharina
K
Markmann
Christian N S
CN
Pedersen
Jens
J
Stougaard
Stig U
SU
Andersen
D017360:Arabidopsis / Q000235:genetics; D057225:Data Mining; D023281:Genomics; D058977:Molecular Sequence Annotation; D058727:RNA, Small Untranslated / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
D058727:RNA, Small Untranslated