swMATH ID: 34369
Software Authors: Kalari KR, Nair AA, Bhavsar JD, O’Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP
Description: MAP-RSeq: The Mayo Analysis Pipeline for RNA Seq: A comprehensive system for RNA-Sequencing data analysis. RNA-Sequencing (RNA-Seq) technology is information-rich; the breadth of information gained spans from large structural changes to single nucleotide variants (SNVs). By efficiently analyzing RNA-Seq data, we can query and obtain a variety of genomic features, such as gene expression, novel and fusion transcripts, alternative splice sites, long non-coding and circular RNAs, SNVs, etc. Most RNA-Seq bioinformatics tools output one or two genomic features for downstream analysis, but so far there have been no comprehensive workflows that can be used to obtain a number of features from RNA-Seq data. To address this shortfall, Mayo Clinic has developed MAP-RSeq – a computational workflow that leverages data from an RNA-Seq experiment to provide comprehensive reports on genomic features for secondary data analysis.
Homepage: http://bioinformaticstools.mayo.edu/research/maprseq/
Related Software: BWA; BatMeth; PSAR-Align; CAP-miRSeq; Pash; Socrates; CUSHAW; MapSplice; Bowtie 2; BSMAP; Bismark; BS Seeker; HIVE-hexagon; PatternHunter; SHRiMP; Soap; STAR
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