shortran: a pipeline for small RNA-seq data analysis

被引：18

作者：

Gupta, Vikas ^{[1
,2
]}

Markmann, Katharina ^{[1
]}

Pedersen, Christian N. S. ^{[2
]}

Stougaard, Jens ^{[1
]}

Andersen, Stig U. ^{[1
]}

机构：

[1] Aarhus Univ, Ctr Carbohydrate Recognit & Signalling, Dept Mol Biol & Genet, DK-8000 Aarhus C, Denmark

[2] Aarhus Univ, Bioinformat Res Ctr, DK-8000 Aarhus C, Denmark

来源：

BIOINFORMATICS | 2012年 / 28卷 / 20期

基金：

新加坡国家研究基金会;

关键词：

ARABIDOPSIS; SEQUENCES; TOOL;

D O I：

10.1093/bioinformatics/bts496

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2698 / 2700

页数：3

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