Differential analysis of gene regulation at transcript resolution with RNA-seq




Differential analysis of gene regulation at transcript resolution with RNA-seq by Cole Trapnell, David G Hendrickson, Martin Sauvageau, Loyal Goff, John L Rinn & Lior Pachter published in Nature Biotechnology (2012) doi:10.1038/nbt.2450 Abstract Differential analysis of gene and transcript expression using high-throughput RNA sequencing (RNA-seq) is complicated by several sources of measurement variability and poses […]






FRT-seq: Amplification-free, strand-specific, transcriptome sequencing




FRT-seq: Amplification-free, strand-specific, transcriptome sequencing by Lira Mamanova et. al. published in Nat Methods. 2010 February; 7(2): 130–132. Abstract We report an alternative approach to transcriptome sequencing for the Illumina Genome Analyzer, in which the reverse transcription reaction takes place on the flowcell. No amplification is performed during the library preparation, so PCR biases and […]






Mapping and quantifying mammalian transcriptomes by RNA-Seq




Mapping and quantifying mammalian transcriptomes by RNA-Seq by Mortazavi, A. et. al. published in Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30. Abstract We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence […]






A mixed model approach for joint genetic analysis of alternatively spliced transcript isoforms using RNA-Seq data




A mixed model approach for joint genetic analysis of alternatively spliced transcript isoforms using RNA-Seq data by Barbara Rakitsch, Christoph Lippert, Hande Topa, Karsten Borgwardt, Antti Honkela, Oliver Stegle, published on the pre-print server arXiv and profiled at Haldane’s Sieve blog in October 2012. Abstract RNA-Seq technology allows for studying the transcriptional state of the cell […]






Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript




Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript by Matteo Benelli, Chiara Pescucci, Giuseppina Marseglia, Marco Severgnini, Francesca Torricelli and Alberto Magi published in Bioinformatics October 2012. Abstract Motivation: The discovery of novel gene fusions can lead to a better comprehension of cancer progression and development. The emergence of deep sequencing of trancriptome, […]






Detecting differential usage of exons from RNA-seq data




Detecting differential usage of exons from RNA-seq data by Simon Anders, Alejandro Reyes and Wolfgang Huber published in Genome Research, 2012 22: 2008-2017 Abstract RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential […]






Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads




Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads, by Wei Li and Tao Jiang from University of California, Riverside, CA, USA and Tsinghua University, Beijing, China. Abstract Motivation: RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually […]