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chevron_left Read alignment Normalization Gene fusion detection Bioinformatics workflows Novel transcript quantification Variant detection Circos plot generation chevron_right
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MAP-RSEQ specifications


Unique identifier OMICS_04793
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Python, R
Computer skills Advanced
Version 1.2.1
Stability Stable
Maintained Yes


No version available



  • person_outline Jean-Pierre Kocher
  • person_outline Matthew Bockol

Publication for MAP-RSEQ

MAP-RSEQ citations


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] ies were prepared (Illumina TruSeq RNA v2) and run on the Illumina High Seq-2000 for 101 bp paired end reads in the Mayo Clinic Medical Genomics Core. Gene expression profiles were obtained using the MAP-RSeq v.1.2.1 workflow, the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with TopHat 2.0.6 against the human hg19 genome build and gene counts with the HTSeq software 0.5.3p9 ( […]


YAP associated chromosomal instability and cholangiocarcinoma in mice

PMCID: 5814182
PMID: 29464042
DOI: 10.18632/oncotarget.23638

[…] alysis was performed by the Mayo Bioinformatics Core Facility to determine differential expression of mouse tumor tissue and adjacent liver tissue. The processing of the mRNA data was performed using MAP-RSeq (v1.2.1.3) []. MAP-RSeq consists of the following steps: alignment, quality control, obtaining genomic features per sample and finally summarizing the data across samples. The pipeline provid […]


Influence of omega 3 fatty acids on skeletal muscle protein metabolism and mitochondrial bioenergetics in older adults

PMCID: 5425117
PMID: 28379838
DOI: 10.18632/aging.101210

[…] a HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.0.12 data collection software. Base-calling was performed using Illumina's RTA version The RNA-Seq data was analyzed using MAP-RSeq v.1.2.1 [], the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with TopHat 2.0.6 [] against the hg19 genome build and gene counts with the HTSeq software 0.5.3p9 (http://ww […]


Model based unsupervised learning informs metformin induced cell migration inhibition through an AMPK independent mechanism in breast cancer

PMCID: 5432329
PMID: 28423712
DOI: 10.18632/oncotarget.16109

[…] Raw Fastq files for 384 RNA-seq single cells were obtained and processed through the MAP-RSeq workflow [] to obtain binary alignment map (BAM) files, summary alignment statistics, and quality control visualizations of mapped reads for each single cell. Paired-end RNA-seq reads were al […]


ABCA7 loss of function variants, expression, and neurologic disease risk

PMCID: 5217615
PMID: 28097223
DOI: 10.1212/NXG.0000000000000126

[…] bution were determined on an Agilent Bioanalyzer DNA 1000 chip. Samples underwent 101-bp paired-end sequencing on Illumina HiSeq2000 sequencers. RNAseq measures were processed through the Mayo Clinic MAP-RSeq pipeline. Indexed bam files were used for visualizing alignments in Integrative Genomics Viewer. […]


Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy

PMCID: 5270622
PMID: 28118661
DOI: 10.1167/iovs.16-20900
call_split See protocol

[…] Whole transcriptomic sequencing data from each tissue sample was analyzed using a comprehensive computational program called the Mayo Analysis Pipeline for RNA Sequencing (MAP-RSeq) (Mayo Clinic, Rochester, MN, USA) to align, assess, and deliver multiple genomic features. MAP-RSeq uses a variety of freely available bioinformatics tools along with in-house developed meth […]

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MAP-RSEQ institution(s)
Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
MAP-RSEQ funding source(s)
Supported by the Mayo Clinic Center for Individualized Medicine (CIM) and Eveleigh family career Development award.

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