Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq transcript assembly evaluation

ABSTRACT: 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 .

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Paul Bertone

PROVIDER: E-MTAB-1730 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström Pär G PG Steijger Tamara T Sipos Botond B Grant Gregory R GR Kahles André A Rätsch Gunnar G Goldman Nick N Hubbard Tim J TJ Harrow Jennifer J Guigó Roderic R Bertone Paul P

Nature methods 20131103 12

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 p ...[more]

PMID: 24185836

Dataset Information

RNA-seq transcript assembly evaluation

Publications

Systematic evaluation of spliced alignment programs for RNA-seq data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Similar Datasets

ChIP-seq on Olig2, Ascl1, Tcf3, Max, NFI, Sox2, Sox9 and Sox21 in mouse neural stem cells
2014-09-19 | E-MTAB-2228 | biostudies-arrayexpress

Strand-specific RNA-Seq of rRNA-depleted total RNA from common types of cultured or uncultured primary cells of different haemopoetic lineages from healthy individuals in the BLUEPRINT epigenome project
2015-09-30 | E-MTAB-3827 | biostudies-arrayexpress

Signatures of selection in the stickleback transcriptome.
2014-12-03 | E-MTAB-3099 | biostudies-arrayexpress

Breed gene expression differences in young offspring chicken with Affymetrix Chicken Gene Chip
2011-05-10 | E-MTAB-644 | biostudies-arrayexpress

Breed gene expression differences in adult parent chicken with Affymetrix Chicken Gene Chip
2011-05-10 | E-MTAB-645 | biostudies-arrayexpress

EGAS00001000195-4-sc-20120308 - samples
| EGAD00001000138 | EGA

Defining the microbial response to colitis through integrated host and microbiome profiling: Replication data set
2015-12-31 | E-MTAB-4082 | biostudies-arrayexpress