Tuxedo specifications

Information


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

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Maintainer


  • person_outline Cole Trapnell <>

Tuxedo article

Tuxedo citations

 (15)
2018
PMCID: 5805368

[…] to our assembled contigs using quast [34, 68]. 79.3% bases of the reference genome could be aligned in the new assembly., using available mrna-seq datasets [34], transcripts were identified by the tuxedo suite. initial mapping with tophat was followed by transcript annotation with cufflinks [69]. transcript similarity was estimated using blast2go., total rna isolated via the trizol method […]

2017
PMCID: 5769612

[…] trimmed using the fqtrim (ccb.jhu.edu/software/fqtrim/) software to remove ambiguous bases from the reads. read alignment and differential gene expression was performed using the programs from the tuxedo rna-seq tool pipeline. the trimmed reads were then aligned to the mouse genome (version mm10/grcm38) and the hg19 human genome (when necessary) using the tophat aligner […]

2017
PMCID: 5653659

[…] pooled prior to sequencing. sequencing was carried out as paired-end 2 × 25 bp with 8 additional cycles for each index. alignment of the reads and calculation of gene expression was done through the tuxedo pipeline (tophat, cuffquand, cuffnorm)62. gene expression was expressed as reads per kilobase exon model per million mapped reads (rpkm)., the bulk rna-seq results were normalized by the total […]

2017
PMCID: 5666786

[…] usa) at the beijing genomics institute collaborative genome center at the children’s hospital of philadelphia ([email protected], philadelphia, pa, usa) and has been described before [18]., elements of the tuxedo suite pipeline [60] were used to analyze the rna-seq data. each of the fastq files was aligned to the hg19 build of the human genome with cufflinks [61,62], and quality-control and result […]

2017
PMCID: 5613355

[…] hepg2 cells [57] produced by caltech were used:, wgencodecaltechrnaseqhepg2r1x75dfastqrep1.fastq.gz., wgencodecaltechrnaseqhepg2r1x75dfastqrep2.fastq.gz., the reads were mapped with tophat from the tuxedo suite package [59] using default settings. the transcript assembly from both replicates was carried out in the rna pipeline in seqmonk, and the transcript list from both replicates was merged. […]

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.

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