MMSEQ protocols

MMSEQ specifications

Information


Unique identifier OMICS_01280
Name MMSEQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ+FASTA
Operating system Unix/Linux, Mac OS
Programming languages C, C++, R, Ruby, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.10
Stability Stable
Requirements Boost C++ libraries, GNU Scientific Library, Armadillo C++ linear algebra library, SAMtools library
Maintained Yes

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Documentation


Maintainer


  • person_outline Ernest Turro <>

Publications for MMSEQ

MMSEQ IN pipelines

 (8)
2018
PMCID: 5844893
PMID: 29523860
DOI: 10.1038/s41598-018-22753-4

[…] of mammalian transcriptomes. for differential expression analysis, cummerbund was employed to perform statistical analyses of gene expression profiles. for allele-specific expression analysis, mmseq was then implemented to estimate allelic imbalance and deconvolve the alignment of reads to diploid transcripts derived from diploid genomic sequences and ensembl gene annotation 74 following […]

2018
PMCID: 5910421
PMID: 29679052
DOI: 10.1038/s41598-018-24544-3

[…] mouse transcriptomes are based on wellcome trust mouse genomes project release22., in order to calculate gene expression level for f0 and allele specific expression for the f1 reads we have used mmseq23 which uses a bayesian approach to count reads to alleles even in the presence of low number of mutations. after obtaining read count for each gene we have normalized read count according […]

2015
PMCID: 4512258
PMID: 26140685
DOI: 10.7554/eLife.07860.022

[…] al., 2013). for each mapped rna-seq library, we then estimated the expression level of each transcript with its respective error, for each allele in a cast/eij×c57bl/6j diploid transcriptome using mmseq (turro et al., 2011). finally, we developed a statistical model testing for genomic imprinting at the level of each transcript, while taking into account the effects of cross, sex, and age […]

2015
PMCID: 4512258
PMID: 26140685
DOI: 10.7554/eLife.07860.022

[…] (e.g., roberts and pachter, 2013). following that, we estimated the expression levels with their respective uncertainties of each transcript in our c57bl/6j, cast/eij diploid transcriptome using mmseq (turro et al., 2011). mmseq uses a bayesian model for estimating expression levels and therefore computes a posterior distribution of the expression levels of each transcript in fragment per […]

2015
PMCID: 4512258
PMID: 26140685
DOI: 10.7554/eLife.07860.022

[…] 2013). following that, we estimated the expression levels with their respective uncertainties of each transcript in our c57bl/6j, cast/eij diploid transcriptome using mmseq (turro et al., 2011). mmseq uses a bayesian model for estimating expression levels and therefore computes a posterior distribution of the expression levels of each transcript in fragment per kilobase per million (fpkm) […]

MMSEQ institution(s)
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, NHS Blood and Transplant, Cambridge, UK; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal QC, Canada
MMSEQ funding source(s)
Supported by Cancer Research UK grant C14303/A10825, the Cambridge Biomedical Research Centre, by UK BBSRC grant BB/E020372/1 and a Team Grant from the Fonds de recherche du Quebec—Nature et technologies.

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