Pubblicazioni

Autori:

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.

Titolo:

Systematic evaluation of spliced alignment programs for RNA-seq data

Anno:

2013

Tipologia prodotto:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Lingua:

Inglese

Referee:

No

Nome rivista:

NATURE METHODS

ISSN Rivista:

1548-7091

N° Volume:

10

Numero o Fascicolo:

12

Intervallo pagine:

1185-1191

Parole chiave:

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

Breve descrizione dei contenuti:

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.

Id prodotto:

97869

Handle IRIS:

11562/963851

ultima modifica:

12 novembre 2022

Citazione bibliografica:

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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