Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T. J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Stevenson, B. J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B. J., Wu, J., Wu, T. D., Zeller, G., Zerbino, D., Zhang, M. Q. (November 2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. ISSN 15487091 (ISSN)
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Abstract
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data. © 2013 Nature America, Inc.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription bioinformatics > genomics and proteomics > genetics & nucleic acid processing |
| CSHL Authors: | |
| Communities: | CSHL labs > Gingeras lab CSHL labs > Zhang lab CSHL labs > Krainer lab |
| Depositing User: | Matt Covey |
| Date: | November 2013 |
| Date Deposited: | 23 Dec 2013 19:59 |
| Last Modified: | 03 Oct 2019 14:46 |
| PMCID: | PMC3851240 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/29160 |
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