Benchmarking RNA-Seq quantification tools

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Volumn , Issue , 2013, Pages 647-650

  Chandramohan, Raghu ^a   Wu, Po Yen ^a   Phan, John H ^b   Wang, May D ^b  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Emory University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION PROFILE; ROOT-MEAN SQUARE DEVIATION; TRANSCRIPTOMES; TRANSCRIPTOMICS;

ESTIMATION; GENE EXPRESSION; POLYMERASE CHAIN REACTION; TOOLS;

RNA;

ISOPROTEIN; MESSENGER RNA; TRANSCRIPTOME;

COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; QUALITY CONTROL; SEQUENCE ANALYSIS; STANDARDS;

BENCHMARKING; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROTEIN ISOFORMS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 84886523027     PISSN: 1557170X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/EMBC.2013.6609583     Document Type: Conference Paper

References (12)

1. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq, " Nature methods, vol. 5, pp. 621-628, 2008.
2. J. C. Marioni, C. E. Mason, S. M. Mane, M. Stephens, and Y. Gilad, "RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays, " Genome research, vol. 18, pp. 1509-1517, 2008.
3. S. Lee, C. H. Seo, B. Lim, J. O. Yang, J. Oh, M. Kim, S. Lee, B. Lee, C. Kang, and S. Lee, "Accurate quantification of transcriptome from RNA-Seq data by effective length normalization, " Nucleic acids research, vol. 39, pp. e9-e9, 2011.
4. U. Nagalakshmi, Z. Wang, K. Waern, C. Shou, D. Raha, M. Gerstein, and M. Snyder, "The transcriptional landscape of the yeast genome defined by RNA sequencing, " Science, vol. 320, pp. 1344-1349, 2008.
5. E. T. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. F. Kingsmore, G. P. Schroth, and C. B. Burge, "Alternative isoform regulation in human tissue transcriptomes, " Nature, vol. 456, pp. 470-476, 2008.
6. M. Garber, M. G. Grabherr, M. Guttman, and C. Trapnell, "Computational methods for transcriptome annotation and quantification using RNA-seq, " Nature methods, vol. 8, pp. 469-477, 2011.
7. B. Li and C. N. Dewey, "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, " BMC Bioinformatics, vol. 12, p. 323, 2011.
8. M. Nicolae, S.Mangul, I. Mandoiu, and A. Zelikovsky, "Estimation of alternative splicing isoform frequencies from RNA-Seq data, " Algorithms in Bioinformatics, pp. 202-214, 2010.
9. C. Trapnell, B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. Van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter, "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, " Nature biotechnology, vol. 28, pp. 511-515, 2010.
10. L. Shi, L. H. Reid, W. D. Jones, R. Shippy, J. A. Warrington, S. C. Baker, P. J. Collins, F. de Longueville, E. S. Kawasaki, and K. Y. Lee, "The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements, " Nature biotechnology, vol. 24, pp. 1151-1161, 2006.
11. C. Trapnell, L. Pachter, and S. L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq, " Bioinformatics, vol. 25, pp. 1105-1111, 2009.
12. B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, " Genome Biol, vol. 10, p. R25, 2009.