Tuxedo statistics

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Tuxedo specifications


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
TopHat, Cufflink
Maintained Yes


No version available


  • person_outline Cole Trapnell

Publication for Tuxedo

Tuxedo citations


Systematic pan cancer analysis of somatic allele frequency

Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] luded 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. […]


Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

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

[…] sing tools such as DiffSplice and MATS, respectively. Experimental designs containing multiple groups or confounding factors would require a tool that can model design matrices such as JunctionSeq or Tuxedo 2. An overview of the available tools for differential alternative splicing analysis is shown in . RNA-seq analysis can generate hypotheses of novel and known splice variants and it is advisabl […]


Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

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

[…] 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 []. Th […]


A Novel S100A8/A9 Induced Fingerprint of Mesenchymal Stem Cells associated with Enhanced Wound Healing

Sci Rep
PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9
call_split See protocol

[…] ce 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 was […]


Blocking negative effects of senescence in human skin fibroblasts with a plant extract

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

[…] 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.Transcr […]


Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma

BMC Syst Biol
PMCID: 5883534
PMID: 29615030
DOI: 10.1186/s12918-018-0554-1
call_split See protocol

[…] Reference Consortium GRCh38 using Bowtie alignment with an extended Burrows-Wheeler indexing for an ultrafast memory efficient alignment within the Tuxedo suite followed by Tophat to account for splice-isoforms [, ]. Read counts were scaled via the median of the geometric means of fragment counts across all libraries. Transcri […]


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