Benchmarking of available tools for the estimation of isoform-level transcript abundances from RNA-seq data. Benchmarking of available tools for the estimation of isoform-level transcript abundances from RNA-seq data

The project is part of an effort at the benchmarking of available tools for the estimation of isoform-level transcript abundances from RNA-seq data, a question of high current interest in high-throughput mRNA expression profiling. Data associated with this project include those from RNA and RNA 3' end sequencing experiments with human (Jurkat) and murine (NIH-3T3) cell lines as well as in silico-generated read sequences generated with Flux Simulator (doi:10.1093/nar/gks666; available at http://sammeth.net/confluence/display/SIM/Home). In particular, the following datasets are provided: raw short read data in FASTQ format and processed genome alignments in BAM format (used as input to benchmarked tools).