This is the Linux app named PRADA whose latest release can be downloaded as PRADA.zip. It can be run online in the free hosting provider OnWorks for workstations.
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PRADA
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DESCRIPTION
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification.
PRADA currently supports 7 modules to process and identify abnormalities from RNAseq data:
preprocess: Generates aligned and recalibrated BAM files.
expression: Generates gene expression (RPKM) and quality metrics.
fusion: Identifies candidate gene fusions.
guess-ft: Supervised search for fusion transcripts.
guess-if: Supervised search for intragenic fusions.
homology: Calculates homology between given two genes.
frame: Predicts functional consequence of fusion transcript
Features
- PRADA is written in python programing language and intended to run in a command line environment on UNIX or LINUX operating systems.
- Detail description of installation steps and the usage of each module with examples is available in the documentation at https://sourceforge.net/p/prada/wiki/Home/attachment/pyPRADA.pdf
- The hg19 reference files are available to download at http://bioinformatics.mdanderson.org/Software/PRADA/
- To remove fusion artifacts, we filter out genes with multiple partners in the same sample and homology.
Categories
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