TopHat statistics

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TopHat specifications


Unique identifier OMICS_01257
Name TopHat
Alternative name TopHat2
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
Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Maintained Yes




No version available



  • person_outline Cole Trapnell

Publications for TopHat

TopHat citations


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] reads in the Mayo Clinic Medical Genomics Core. Gene expression profiles were obtained using the MAP-RSeq v.1.2.1 workflow, the Mayo Bioinformatics Core pipeline. MAP-RSeq consists of alignment with TopHat 2.0.6 against the human hg19 genome build and gene counts with the HTSeq software 0.5.3p9 ( using gene annotation files obtained fr […]


Elucidating the genetic architecture of reproductive ageing in the Japanese population

Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] read qualities in those bases as compared to the remainder of the read. Trimmed reads that passed the Trimmomatic selection criteria were then aligned to the rn6 build of the rat genome with Bowtie2/Tophat2, using default parameters. Aligned reads were assigned to gene-level genomic features of the Ensembl 83 annotation set using the Rsubread featureCounts R function with countMultiMappingReads a […]


Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A

Nat Commun
PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] ucing conditions (Supplementary Table¬†). 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 genome. Differential gene expression was then analysed with ReadXplorer 2.0 including the DESeq package. The results (Fig.¬†) cl […]


FACS Seq analysis of Pax3 derived cells identifies non myogenic lineages in the embryonic forelimb

Sci Rep
PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1
call_split See protocol

[…] base calling, and read-quality filtering were done using the Casava pipeline version 1.8.2 (Illumina). Each sample was processed and analyzed with the same methods. After filtering low quality reads TopHat version 2.1.0 was used to align all reads to the mm10 genome with default parameters and to identify splice junctions,. HTseq was used to create count tables from tophat2 aligned reads. DESeq2 […]


Genomic alterations of ground glass nodular lung adenocarcinoma

Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] The reads from the FASTQ files were mapped against the hg19 human reference genome using TopHat version 2.0.6 ( Raw read counts mapped onto genes were measured with the BAM format file by HTSeq version 0.6.1. Then a total of 18,161 coding genes were subjected […]


Integrated analysis of hepatic mRNA and miRNA profiles identified molecular networks and potential biomarkers of NAFLD

Sci Rep
PMCID: 5955949
PMID: 29769539
DOI: 10.1038/s41598-018-25743-8

[…] a using the FastQC tool. To obtain high-quality, clean data for analysis, adaptor sequence trimming and removal of low-quality reads were performed. Clean reads were aligned with the rat genome using TopHat v2.1.1. Based on the ultra-high throughput short-read aligner Bowtie, TopHat aligned RNA-Seq reads to reference genomes and analyzed the mapping reads to determine possible splice junctions bet […]


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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.
Anonymous user #60's avatar image No country

Anonymous user #60

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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.