Dataset Information
PRADA: pipeline for RNA sequencing data analysis.
Ontology highlight
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.orgSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Torres-Garcia W
PROVIDER: S-EPMC4103589 | biostudies-literature | 2014 Aug
REPOSITORIES: biostudies-literature
Publications
PRADA: pipeline for RNA sequencing data analysis.
Bioinformatics (Oxford, England) 20140401 15
<h4>Summary</h4>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 m ...[more]