MMSEQ protocols

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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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Maintainer


  • person_outline Ernest Turro <>

Publications for MMSEQ

MMSEQ in pipelines

 (16)
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

[…] both mouse transcriptomes are based on wellcome trust mouse genomes project release., in order to calculate gene expression level for f0 and allele specific expression for the f1 reads we have used mmseq 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 […]

2017
PMCID: 5442720
PMID: 28205406
DOI: 10.1002/sctm.16-0229

[…] clontech smart seq kit . quality control, trimming, alignment, and differential expression analysis using a bayesian linear mixed effects model was performed as described elsewhere , using bowtie, mmseq, and mmdif , , . differentially expressed genes and transcripts were required to have a posterior probability >0.3. the rna‐sequencing (rna‐seq) data was submitted to the gene expression […]

2017
PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] adapters. trimmed reads were aligned to the ensembl v70 (ref. ) human transcriptome with bowtie 1.0.1 (ref. ), with parameters ‘-a --best --strata -s -m 100 -x 500 --chunkmbs 256 --nofw -fr’. mmseq 1.0.8a (refs , ), and was used with default parameters to quantify gene expression. genes with posterior probability>0.5 (calculated by mmdiff), absolute fold change >2 and fragments per […]

2016
PMCID: 5035046
PMID: 27662371
DOI: 10.1371/journal.pone.0163663

[…] per million mapped reads). the reference genome and gene annotations were retrieved from the ensembl database. the genome analysis toolkit (gatk) was used for snp finding and genotype determination. mmseq was applied for allelic-specific-expression (ase) analysis. monoallelic gene expression was defined as log(ma/pa) larger than 0.5 or less than -0.5. the identities of monoallelically-expressed […]


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MMSEQ in publications

 (32)
PMCID: 5658514
PMID: 28985526
DOI: 10.1016/j.stem.2017.09.004

[…] bowtie were used for chip-seq and rna-seq, respectively, to align sequencing reads to the mouse genome (mm9) using default parameters. for rna-seq transcript quantification was performed using the mmseq package and after setting a threshold of at least 50 reads over the gene body in either serum or 2i the deseq2-package was used to call differentially expressed genes (log2-fold change > 1 […]

PMCID: 5554779
PMID: 28768205
DOI: 10.1016/j.celrep.2017.07.025

[…] we explored a transcript-centric approach, which considers transcripts as whole units, to facilitate the integration with the proteomic dataset. we first estimated transcript expression levels with mmseq () and then used its companion tool mmdiff () to identify both differentially expressed genes and differentially used transcripts. genes with differential transcript usage (dtu) are defined […]

PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] adapters. trimmed reads were aligned to the ensembl v70 (ref. ) human transcriptome with bowtie 1.0.1 (ref. ), with parameters ‘-a --best --strata -s -m 100 -x 500 --chunkmbs 256 --nofw -fr’. mmseq 1.0.8a (refs , ), and was used with default parameters to quantify gene expression. genes with posterior probability>0.5 (calculated by mmdiff), absolute fold change >2 and fragments per […]

PMCID: 5870700
PMID: 28881996
DOI: 10.1093/bioinformatics/btx262

[…] community began developing principled inference methodologies to allow accurate transcript-level quantification in the presence of multi-mapping reads. tools such as cufflinks (), rsem (), mmseq () and isoem () provided statistical models by which transcript-level abundance estimates could be inferred. these methodologies principally rely on maximum likelihood estimation to infer […]

PMCID: 5564811
PMID: 28548943
DOI: 10.18632/oncotarget.17765

[…] by certified illumina service providers. the rnaseq raw data were first cleaned by removing reads that were preferentially mapped to a mouse genome (ucsc mm9). transcript expression was estimated by mmseq [] and represented by log2(fpkm). snp and indels were detected by star [] mapping software and gatk [] variant discovery toolkit, and gene fusions were detected by soap fuse [] and defuse []., […]


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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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