kallisto paper summary: Near-optimal RNA-seq quantification

In case you missed it, kallisto, the new RNA-seq quantification method from Lior Pachter‘s group, was one of the biggest highlights from this year’s The Biology of the Genomes conference. kallisto team made the kallisto software immediately available and the preprint describing kallisto was available at arXiv pretty soon after the #BOG15. Near-optimal RNA-Seq quantification, Nicolas Bray, […]

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 […]

Bayesian Approach to Single-Cell RNA-Seq Differential Expression Analysis

Just a few weeks ago Nature Methods published an interesting paper on Bayesian approach that takes care of technical variations in Single Cell RNA-seq data and perform differential expression analysis . This is one of many interesting papers that came out recently addressing technical variations in single-cell RNA-seq data. Bayesian approach to single-cell differential expression […]

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 […]

Tophat/RNA-seq Analysis Nostalgia

Recently just started playing with TopHat, after a while back, for doing gene expression quantitation using  RNA-seq data and got all nostalgic about RNA-seq analysis over the years. Although there are over 70 short read aligners to choose from, accurately aligning non-contiguos RNA-seq reads and quantifying expression is still challenging.  Only a few of the […]