E-MTAB-1730 - RNA-seq transcript assembly evaluation

Status
Released on 15 July 2013, last updated on 21 April 2014
Organism
Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens
Samples (12)
Protocols (6)
Description
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 .
Experiment types
RNA-seq of coding RNA, co-expression, reference, software variation, species
Contact
Citation
Assessment of transcript reconstruction methods for RNA-seq. Tamara Steijger, Josep F. Abril, Pär G. Engström, Felix Kokocinski, RGASP Consortium, Tim J. Hubbard, Roderic Guigó, Jennifer Harrow, Paul Bertone. Nat Methods 10(12):1177–1184 (2013), Europe PMC 24185836
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1730.idf.txt
Sample and data relationshipE-MTAB-1730.sdrf.txt
Links