MAP-RSEQ statistics

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MAP-RSEQ specifications

Information


Unique identifier OMICS_04793
Name MAP-RSEQ
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

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Documentation


Maintainers


  • person_outline Jean-Pierre Kocher <>
  • person_outline Matthew Bockol <>

Publication for MAP-RSEQ

MAP-RSEQ in publications

 (17)
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] 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 […]

PMCID: 5812288
PMID: 29366785
DOI: 10.1016/j.bbrc.2018.01.092

[…] using hiseq 3000/4000 sequencing kits and hcs v3.3.20 data collection software. base-calling was performed using illumina's rta version 2.5.2., processing of the mrna-seq data was performed using map-rseq workflow (v1.2.0.0) [] and rseqc software (v2.3.2) []. paired-end reads were aligned by tophat (v2.0.12) against the hg19 and mm10 genome build for human and mouse samples []. gene counts […]

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

[…] 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 […]

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

[…] 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 1.17.21.3. 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 […]

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

[…] we sequenced 192 cells at baseline and 192 after metformin treatment, referred to subsequently as baseline cells and metformin-treated cells, respectively. after quality control was performed with map-rseq [], the initial analysis was conducted on normalized gene expression data. the sequencing data showed that 20% of the genes had a reads-per-kilobase-per-million mapped reads (rpkm) measure […]


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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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