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RNA-seq read alignment evaluation

ABSTRACT: To assess the performance of read mapping software for RNA-seq, 26 spliced alignment protocols based on 11 programs and pipelines (BAGET, GEM, GSNAP, GSTRUCT, MapSplice, PALMapper, PASS, ReadsMap, SMALT, STAR and TopHat) were applied to four human and mouse transcriptome data sets.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Homo sapiens

SUBMITTER: Paul Bertone

PROVIDER: E-MTAB-1728 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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