title: MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
abstract: BACKGROUND
  Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data. There is no one-stop shop for transcriptomic genomics. We have developed MAP-RSeq, a comprehensive computational workflow that can be used for obtaining genomic features from transcriptomic sequencing data, for any genome.
  
  
  RESULTS
  For optimization of tools and parameters, MAP-RSeq was validated using both simulated and real datasets. MAP-RSeq workflow consists of six major modules such as alignment of reads, quality assessment of reads, gene expression assessment and exon read counting, identification of expressed single nucleotide variants (SNVs), detection of fusion transcripts, summarization of transcriptomics data and final report. This workflow is available for Human transcriptome analysis and can be easily adapted and used for other genomes. Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies. The results from MAP-RSeq have thus far enabled clinicians and researchers to understand the transcriptomic landscape of diseases for better diagnosis and treatment of patients.
  
  
  CONCLUSIONS
  Our software provides gene counts, exon counts, fusion candidates, expressed single nucleotide variants, mapping statistics, visualizations, and a detailed research data report for RNA-Seq. The workflow can be executed on a standalone virtual machine or on a parallel Sun Grid Engine cluster. The software can be downloaded from http://bioinformaticstools.mayo.edu/research/maprseq/.
authors: Krishna R
authors: KR
authors: Kalari
authors: Asha A
authors: AA
authors: Nair
authors: Jaysheel D
authors: JD
authors: Bhavsar
authors: Daniel R
authors: DR
authors: O'Brien
authors: Jaime I
authors: JI
authors: Davila
authors: Matthew A
authors: MA
authors: Bockol
authors: Jinfu
authors: J
authors: Nie
authors: Xiaojia
authors: X
authors: Tang
authors: Saurabh
authors: S
authors: Baheti
authors: Jay B
authors: JB
authors: Doughty
authors: Sumit
authors: S
authors: Middha
authors: Hugues
authors: H
authors: Sicotte
authors: Aubrey E
authors: AE
authors: Thompson
authors: Yan W
authors: YW
authors: Asmann
authors: Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA. kocher.jeanpierre@mayo.edu.
authors: Jean-Pierre A
authors: JP
authors: Kocher
mesh_terms: D001483:Base Sequence; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006268:Health Facilities; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software