RNA-Skim: new RNA-seq quantitation method that is faster than Sailfish




This is a quick post: summary/thoughts* on the new paper that got accepted at the upcoming ISMB 2014 and published in the special issue of  Bioinformatics. RNA-Skim: a rapid method for RNA-Seq quantification at transcript level  Zhaojun Zhang and Wei Wang is from a duo at UNC and UCLA. (*thoughts are always half baked :)) RNA-Skim is a […]

Sailfish: Alignment-free isoform quantification from RNA-seq reads




Sailfish – the fastest and alignmnet-free isoform-level quantitation of RNA-seq data is now published on Nature Biotechnology. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms, by Rob Patro,Stephen M Mount, & Carl Kingsford Sailfish manuscript was first available in the open preprint server arXiv in August 2013 and now it is in […]

Sailfish: Isoform Quantitation at the Speed of Making a Cup of Coffee




This is a really quick summary of the interesting paper “Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms, by Rob Patro, Stephen M. Mount, Carl Kingsford” that was on arXiv and @Haldanesive early this week. Sailfish is a new computational approach that can quantify isoform level expression using RNA-seq data. What is novel about Sailfish […]