TopHat pipeline

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
Requirements Bowtie, Bowtie-align, Bowtie-inspect, Bowtie-build, samtools
Maintained Yes



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  • person_outline Cole Trapnell <>

Publications for TopHat

TopHat IN pipelines

PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] and chip-seq data shared the same experimental condition—hela cells were treated with egf (100 ng/ml) for 20 min after 48 hr serum starvation. rna-seq data was aligned to the human genome hg19 using tophat. unmapped reads were filtered out. transcripts were assembled by cufflink. differential expression of transcripts was estimated by cuffdiff 9. for chip-seq data, bowtie2 was used for mapping […]

PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] ca, usa). low-quality nucleotides (<q15) from both the 5′- and the 3′-ends were trimmed by using btrim [42]. reads were aligned to the reference genome of btx623 (sbicolor_v1.4_79) [43] by using tophat version 2.0.4 [44]. differentially expressed genes were identified by using cuffdiff version 2.2.0 [45], with the gene models annotated in sbicolor ver1.4 [46]., mapman (3.5.1 r2) software […]

PMCID: 5754085
PMID: 29300744
DOI: 10.1371/journal.pone.0189185

[…] sequences, empty reads, low-quality sequences, and short reads. the high-quality reads were aligned to the phaseolus vulgaris genome (v1.0), available in phytozome (joint genome institute), using tophat2/bowtie2 [21, 22]. reads overlapping with the annotation range of interest were counted for each sample using the “summarizeoverlaps” function [23]. read counting was performed for exonic gene […]

PMCID: 5758557
PMID: 29354030
DOI: 10.3389/fnmol.2017.00433

[…] cord from 95 days old mice (n = 5/group). libraries of template molecules suitable for high throughput dna sequencing were created and reads were mapped onto mm10 assembly of mouse genome using tophat v2.0.14 (kim et al., 2013). quantification of gene expression was performed using htseq v0.6.1 (anders and huber, 2010) and ensembl release 81 database. supervised statistical analysis […]

PMCID: 5758603
PMID: 29354153
DOI: 10.3389/fpls.2017.02226

[…] protocols (trapnell et al., 2012). briefly, raw sequencing data were first evaluated with the fastqc program. all filtered and properly paired reads were then mapped to the arabidopsis genome using tophat. the fragment alignments generated by tophat were then used as input files to be further analyzed through the recommended cufflinks packages to detect the differentially expressed genes […]

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 review

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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.