The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Open accessAbstract
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat .
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Spliced read aligners that have successfully been used for allele-specific alignments in conjunction with SNPsplit include Tophat 18, STAR 14 (Spliced Transcripts Alignment to a Reference) and HISAT2 13.”
From SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes (2016) · cites this paper as [18]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Although qPCR based methods have traditionally been used as a reference 'gold' standard owing to their high sensitivity and dynamic range, it is noteworthy in this context that specific primer selection and protocol calibration are challenging in their own right. 20”
From A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (2014) · cites this paper as [20]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Self-citationSTAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Self-citationMapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
The Diploid Genome Sequence of an Individual Human
Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778
Improving RNA-Seq expression estimates by correcting for fragment bias
Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology · doi:10.1186/gb-2011-12-3-r22 · Cited by 1,725
Self-citationPersonal omics profiling reveals dynamic molecular and medical phenotypes
Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq622 · Cited by 1,193
Research works printed but not linked: 9
- Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB: The GENCODE pseudogene resource. Genome Biol. 2012, 13: R51-10.1186/gb-2012-13-9-r51. · DOI
- Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25: 1105-1111. 10.1093/bioinformatics/btp120. · DOI
- Wu TD, Nacu S: Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010, 26: 873-881. 10.1093/bioinformatics/btq057. · DOI · Paper page
- Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA: Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011, 27: 2518-2528. · DOI
- Zhang Z, Harrison PM, Liu Y, Gerstein M: Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003, 13: 2541-2558. 10.1101/gr.1429003. · DOI
- Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu YM, Cao X, Asangani IA, Kothari V, Prensner JR, Lonigro RJ, Iyer MK, Barrette T, Shanmugam A, Dhanasekaran SM, Palanisamy N, Chinnaiyan AM: Expressed pseudogenes in the transcriptional landscape of human cancers. Cell. 2012, 149: 1622-1634. 10.1016/j.cell.2012.04.041. · DOI
- Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB: Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 2009, 19: 1516-1526. 10.1101/gr.091827.109. · DOI
- Kim D, Salzberg SL: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 2011, 12: R72-10.1186/gb-2011-12-8-r72. · DOI
- Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigo R, Sammeth M: Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic acids Res. 2012
Cited by
Sorted by citations
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Near-optimal probabilistic RNA-seq quantification
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology · doi:10.1038/nbt.3519 · Cited by 9,723
Self-citationTrapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314
Self-citationGenomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma
Hugo, W., Zaretsky, J. M., Sun, L., Song, C., Moreno, B. H., Hu-Lieskovan, S., Berent-Maoz, B., Pang, J., Chmielowski, B., Cherry, G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.065 · Cited by 3,448
Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation
Huang, H., Weng, H., Sun, W., Qin, X., Shi, H., Wu, H., Zhao, B. S., Mesquita, A., Liu, C., Yuan, C. L., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0045-z · Cited by 2,997
Metadata
- Authors
- Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L.
- Affiliations
- Johns Hopkins University (US)
- Broad Institute (US)
- University of California, Berkeley (US)
- Illumina (United States) (US)
- Corresponding author
- Kim, Daehwan
- Venue
- Genome Biology
- Published
- 2013-04-25
- Volume
- 14
- Issue
- 4
- Pages
- R36-R36
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4053844
- OpenAlex
- W2140729960
- Cited by
- 12,668
- References
- 8
- Citations by year
- 2026: 212 · 2025: 393 · 2024: 659 · 2023: 771 · 2022: 1009 · 2021: 1317 · 2020: 1554 · 2019: 1524 · 2018: 1517 · 2017: 1440 · 2016: 1103 · 2015: 729 · 2014: 352 · 2013: 68
- FWCI
- 336.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- University Libraries (University of Maryland) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Digital Repository at the University of Maryland (University of Maryland College Park)
- Funders
- Harvard University
- Johns Hopkins University
- Broad Institute
- National Institutes of Health (HG006677)
- Johns Hopkins Bloomberg School of Public Health
- National Human Genome Research Institute (R01HG006102, R01HG006677)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- RNA-seq alignment, spliced alignment, transcriptome alignment, indels, gene fusion, pseudogenes, repetitive genomes
- MeSH terms
- Humans, Sensitivity and Specificity, Software, Mutagenesis, Insertional, Sequence Alignment, Sequence Analysis, RNA, Gene Duplication, Gene Fusion, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
