TopHat specifications


Unique identifier OMICS_01257
Name TopHat
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
Computer skills Advanced
Version 2.1.1
Stability Stable
Requirements Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Maintained Yes



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  • person_outline Cole Trapnell <>

TopHat articles

TopHat citations

PMCID: 5958101

[…] conditions (supplementary table 13). total rna was collected from fermentations of s. schorii grown in aspm (production) and dpy (non-production) media and sequenced by standard illumina methods. tophat2 was used to map quality-filtered reads onto the s. schorii draft genome19. differential gene expression was then analysed with readxplorer 2.020 including the deseq package21. the results […]

PMCID: 5937035

[…] v2 guide (part #15026495) and sequenced (paired-end with 2 × 100 bp read length) on an illumina hiseq 2500 instrument generating 6 to 37 mio reads per sample. paired-end reads were aligned with tophat (version 2.0.8b) [116] and bowtie2 (version 2.1.0) [117] to human reference genome (hg19) and gencode transcriptome (v19). we estimated the mean insert size and standard deviation […]

PMCID: 5935673

[…] subjected to pairing end sequencing, with 101-nt read length. adaptor and low-quality reads were removed using trimmomatic50. the reads were mapped to the d. melanogaster genome (release 5) using tophat251. differential expression of the genes and transposon insertions was assessed using geometric normalisation. the libraries were aligned to the canonical transposon sequence (flybase). […]

PMCID: 5923294

[…] at the science for life laboratory, stockholm, sweden. data processing was carried out at snic-uppmax, uppsala, sweden58. the generated reads were mapped to the human genome version grch37 using tophat v. 2.0.459. read data were converted to gene counts with the program htseq v. 0.6.160. differential gene expression was assessed using bioconductor deseq. 2 package61 running in r language […]

PMCID: 5923265

[…] were quality checked on an agilent bioanalyzer, pooled at an equimolar ratio and sequenced on a hiseq2500 using 50 bp paired-end chemistry. raw sequencing reads were mapped to the mm9 genome using tophat261 and the ucsc mm9 known gene reference transcript database62. for each sample, reads that overlapped exons of unique entrez genes were annotated using the genomicranges (v1.22.4) package […]

TopHat institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Computer Science, University of Maryland, College Park, MD, USA; Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA; Illumina Inc., San Diego, CA, USA
TopHat funding source(s)
This work is supported in part by the National Human Genome Research Institute (NIH) under grants R01-HG006102 and R01-HG006677.

TopHat reviews

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Arup Ghosh

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A popular tool for RNA-seq alignment but major disadvantages are slow and support discontinued after the launch of HISAT.
Claudia Armenise Quartz Bio's avatar image No country

Claudia Armenise Quartz Bio

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Useful tool to map mRNA-seq reads, i.e. to align reads mapping onto multiple exons. Unfortunately, the support team is not very reactive to fix bugs.