Tuxedo protocols

View Tuxedo computational protocol

Tuxedo statistics

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chevron_left Differential expression Novel transcript quantification Normalization Alternative splicing events identification Known transcript quantification Reference-based transcriptome assembly Spliced read alignment Gene expression visualization chevron_right
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Tuxedo specifications

Information


Unique identifier OMICS_01415
Name Tuxedo
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
TopHat, Cufflink
Maintained Yes

Versioning


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Maintainer


  • person_outline Cole Trapnell <>

Publication for Tuxedo

Tuxedo in pipelines

 (64)
2018
PMCID: 5805368
PMID: 29377900
DOI: 10.1371/journal.pgen.1007183

[…] to our assembled contigs using quast [, ]. 79.3% bases of the reference genome could be aligned in the new assembly., using available mrna-seq datasets [], transcripts were identified by the tuxedo suite. initial mapping with tophat was followed by transcript annotation with cufflinks []. transcript similarity was estimated using blast2go., total rna isolated via the trizol method […]

2018
PMCID: 5895844
PMID: 29675264
DOI: 10.1038/s41514-018-0023-5

[…] et al. in preparation)., library preparation and sequencing were performed on an illumina highseq 2000 platform (gatc biotech ag; konstanz, germany). all analysis steps were done according to the tuxedo suite pipeline. briefly, illumina casava 1.8.2 software was used for base calling. rna-seq reads were aligned to hg19 genome assembly using tophat version 2.0.13 with default parameters., […]

2018
PMCID: 5908059
PMID: 29672525
DOI: 10.1371/journal.pone.0194792

[…] and clustervenn []., differential expression profiles of selected fa genes and cnl class r genes in 22-tissue transcript libraries (bioproject prjna201497) were determined from the output of the tuxedo suite pipeline (bowtie2.1.0, tophat2.0.9 [], cufflinks 2.2.1 [], cuffmerge 2.2.1, cuffdiff 2.2.1) mapped to the pisifera 5 reference genome build assembly and linked to 26,059 gene model []. […]

2018
PMCID: 5915338
PMID: 29707694
DOI: 10.3934/microbiol.2018.1.123

[…] files were generated using the bc12fastq software, version 1.8.4 and provided to the unmc bioinformatics core facility for further analysis. the fastq files for each sample were analyzed using the tuxedo pipeline to find differentially expressed genes. read alignment was done using tophat version 2.0. fpkm values (which measure gene expression levels) were calculated with cufflinks 2.2. […]

2017
PMCID: 5311114
PMID: 28217743
DOI: 10.1128/mSphere.00038-17

[…] were sequenced on an illumina hiseq 2500 instrument. high-throughput sequencing reads were aligned to transcripts from the y. lipolytica clib122 genome () using bowtie2 () and quantified using the tuxedo suite of tools (). a summary of the results of the expression analysis is available in in the supplemental material. gene ontology analysis was performed using funrich (). analysis […]


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Tuxedo in publications

 (271)
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0

[…] from the analyses. for the nmd-analysis, short-living (<1 h half-life) transcripts were identified based on tani et al.,. the gene expression was quantified using the cufflinks package from the tuxedo suite, as we have previously described., allele frequencies within a sample were determined through estimation of the relative abundance of variant over total sequence read counts, expressed […]

PMCID: 5915717
PMID: 29685977
DOI: 10.1098/rstb.2017.0073

[…] junctions. therefore, junctionseq can identify differential splicing patterns of an exon even when the exon has consistent expression over all conditions. alternatively, methods such as cuffdiff 2, tuxedo 2 and miso assign reads to isoform transcripts and therefore model isoform as opposed to exon expression (). while this additional level of complexity in the modelling can be more error prone, […]

PMCID: 5908059
PMID: 29672525
DOI: 10.1371/journal.pone.0194792

[…] and clustervenn []., differential expression profiles of selected fa genes and cnl class r genes in 22-tissue transcript libraries (bioproject prjna201497) were determined from the output of the tuxedo suite pipeline (bowtie2.1.0, tophat2.0.9 [], cufflinks 2.2.1 [], cuffmerge 2.2.1, cuffdiff 2.2.1) mapped to the pisifera 5 reference genome build assembly and linked to 26,059 gene model []. […]

PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9

[…] of adapter sequences using the fastqc program. the phred score of q30 was obtained for all the fastq rnaseq files. following initial analysis, reads that passed the qc were processed using the new tuxedo algorithm,. briefly, rnaseq reads were aligned to the human reference genome hg38 annotation using the hisat2 algorithm and read counting overlapping gene counting overlapping gene features […]

PMCID: 5895844
PMID: 29675264
DOI: 10.1038/s41514-018-0023-5

[…] et al. in preparation)., library preparation and sequencing were performed on an illumina highseq 2000 platform (gatc biotech ag; konstanz, germany). all analysis steps were done according to the tuxedo suite pipeline. briefly, illumina casava 1.8.2 software was used for base calling. rna-seq reads were aligned to hg19 genome assembly using tophat version 2.0.13 with default parameters., […]


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Tuxedo institution(s)
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Computer Science, University of California, Berkeley, CA, USA; Computer Science and Artificial Intelligence Lab, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Mathematics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
Tuxedo funding source(s)
Supported by Director's New Innovator Awards (1DP2OD00667-01) and the Center of Excellence in Genome Science from the US National Human Genome Research Institute.

Tuxedo review

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Gyan Prakash Mishra

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Desktop
This pipeline is deprecated now that is based in cufflinks. The newer version is HISAT-StringTie- Ballgown