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

Status
Last updated on 12 July 2013, released on 15 July 2013
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.
Experiment types
RNA-seq of coding RNA, co-expression, reference, software variation, species
Contact
Citation
Comprehensive assessment of transcript reconstruction methods for RNA-seq. Tamara Steijger, Josep F. Abril, Par G. Engstrom, Felix Kokocinski, Tim J. Hubbard, Roderic Guigo, Jennifer Harrow, Paul Bertone.
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1730.idf.txt
Sample and data relationshipE-MTAB-1730.sdrf.txt
Links