PRADA
| PRADA | ||
| Overview | ||
|---|---|---|
| Description | PRADA is a pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | |
| Development Information | ||
| Language | Python | |
| Current Version | 1.1 | |
| Platforms | Un*x (OpenPBS) | |
| License | MIT | |
| Status | Active | |
| Last Updated | April 2013 | |
| References | ||
| Citations | No Formal Publications | |
| Help and Support | ||
| Contact | Roel Verhaak | |
| Discussion | Project Forum | |
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. The BAM files generated by the pipeline are readily compatible with different tools for mutation calling and to obtain read counts for further downstream analysis.
Contents[hide] |
Modules
PRADA currently supports 6 modules to process and identify abnormalities from RNAseq data:
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preprocess : Generates aligned and recalibrated BAM files. fusion : Identifies candidate gene fusions. guess-ft : Supervised search for fusion transcripts. guess-if : Supervised search for intragenic rearrangements. homology : Calculates homology between given two genes. frame : Predicts functional consequence of fusion transcript
Documentation
Detail description of installation steps and the usage of each module with examples is available in the documentation.
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