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Bioinformatics DOI:10.1093/bioinformatics/btu169

PRADA: pipeline for RNA sequencing data analysis.

Publication TypeJournal Article
Year of Publication2014
AuthorsTorres-García, W, Zheng, S, Sivachenko, A, Vegesna, R, Wang, Q, Yao, R, Berger, MF, Weinstein, JN, Getz, G, Verhaak, RGW
JournalBioinformatics
Volume30
Issue15
Pages2224-6
Date Published2014 Aug 01
ISSN1367-4811
KeywordsBase Sequence, Gene Fusion, Genome, Human, Humans, Neoplasms, Oligonucleotide Array Sequence Analysis, RNA, Messenger, Sequence Analysis, RNA, Software, Statistics as Topic
Abstract

SUMMARY: Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification. PRADA uses a dual-mapping strategy that increases sensitivity and refines the analytical endpoints. PRADA has been used extensively and successfully in the glioblastoma and renal clear cell projects of The Cancer Genome Atlas program.

AVAILABILITY AND IMPLEMENTATION: http://sourceforge.net/projects/prada/

CONTACT: gadgetz@broadinstitute.org or rverhaak@mdanderson.org

SUPPLEMENTARY INFORMATION:  Supplementary data are available at Bioinformatics online.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=24695405
DOI10.1093/bioinformatics/btu169
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/24695405?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID24695405
PubMed Central IDPMC4103589
Grant ListP30 CA016672 / CA / NCI NIH HHS / United States
CA143883 / CA / NCI NIH HHS / United States