Publications

Authors:

Engström, Pg; Steijger, T; Sipos, B; Grant, Gr; Kahles, A; Alioto, T; Behr, J; Bertone, P; Bohnert, R; Campagna, D; Davis CA, Dobin A; Engström, Pg; Gingeras, Tr; Goldman, N; Grant GR, Guigó R; Harrow J, Hubbard TJ; Jean G, Kahles A; Kosarev, P; Li, S; Liu, J; Mason, Ce; Molodtsov, V; Ning, Z; Ponstingl, H; Prins, Jf; Rätsch, G; Ribeca, P; Cseledtsov, I; Sipos, B; Solovyev, V; Steijger, T; Valle, G; Vitulo, Nicola; Wang, K; Wu, Td; Zeller, G; Rätsch, G; Goldman, N; Hubbard, Tj; Harrow, J; Guigó, R; Bertone, P.

Title:

Systematic evaluation of spliced alignment programs for RNA-seq data

Year:

2013

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Referee:

No

Name of journal:

NATURE METHODS

ISSN of journal:

1548-7091

N° Volume:

10

Number or Folder:

12

Page numbers:

1185-1191

Keyword:

Animals; Chromosome Mapping; Computational Biology; Exons; False Positive Reactions; High-Throughput Nucleotide Sequencing; Humans; K562 Cells; Mice; RNA, Messenger; Reproducibility of Results; Sequence Alignment; Sequence Analysis, RNA; Software; RNA Splicing

Short description of contents:

High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.

Product ID:

97869

Handle IRIS:

11562/963851

Last Modified:

November 12, 2022

Bibliographic citation:

Engström, Pg; Steijger, T; Sipos, B; Grant, Gr; Kahles, A; Alioto, T; Behr, J; Bertone, P; Bohnert, R; Campagna, D; Davis CA, Dobin A; Engström, Pg; Gingeras, Tr; Goldman, N; Grant GR, Guigó R; Harrow J, Hubbard TJ; Jean G, Kahles A; Kosarev, P; Li, S; Liu, J; Mason, Ce; Molodtsov, V; Ning, Z; Ponstingl, H; Prins, Jf; Rätsch, G; Ribeca, P; Cseledtsov, I; Sipos, B; Solovyev, V; Steijger, T; Valle, G; Vitulo, Nicola; Wang, K; Wu, Td; Zeller, G; Rätsch, G; Goldman, N; Hubbard, Tj; Harrow, J; Guigó, R; Bertone, P., Systematic evaluation of spliced alignment programs for RNA-seq data «NATURE METHODS» , vol. 10 , n. 12 , 2013 , pp. 1185-1191

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