E-MTAB-1730 - RNA-seq transcript assembly evaluation
Released on 15 July 2013, last updated on 27 November 2015
Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens
To assess the performance of computational methods for exon identification, transcript reconstruction and expression level quantification from RNA-seq data, 24 protocol variants of 14 independent software programs (AUGUSTUS, Cufflinks, Exonerate, GSTRUCT, iReckon, mGene, mTim, NextGeneid, Oases, SLIDE, Transomics, Trembly, Tromer and Velvet) were evaluated against transcriptome data from human cells and two model organisms. The following supplementary data files are also available from ArrayExpress at http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1730/files/ : (1) Reference annotation used in the study, (2) Alignments used for reference annotation, (3) Predicted exons and transcript models submitted for evaluation and (4) NanoString nCounter probes and detection counts. Each file is described in greater detail in file http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1730/files/E-MTAB-1730_supplemental_files.xlsx .
RNA-seq of coding RNA, co-expression, reference, software variation, species
Assessment of transcript reconstruction methods for RNA-seq. Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P, RGASP Consortium. :1177-1184 (2013), Europe PMC 24185837
Systematic evaluation of spliced alignment programs for RNA-seq data. Pär Engström, Tamara Steijger, Botond Sipos, Gregory R. Grant, RGASP Consortium, Nick Goldman, Tim J. Hubbard, Jennifer Harrow, Roderic Guigó, Paul Bertone. Nat Methods 10(12):1185-1191 (2013), Europe PMC 24185836