Cataloging Splice Junctions in all Human RNA-seq data from Sequence Read Archive




One of the biggest sources of complexity in transcriptomes come from ubiquitous splicing. Our knowledge about the prevalence of alternative splicing has greatly increased from our ability to directly sequence the transcritome by using RNA-seq technology. Granted that to fully characterize the isoforms resulting from splicing, one needs long-read transcriptome sequencing. However, the abundance of […]

Paper Summary: Systematic bias and batch effects in single-cell RNA-Seq data




Single Cell RNA-seq technology has gained a lot of traction in the last few years, as it can help address a variety of interesting biological problems, ranging from studying development to cancer heterogeneity.  Since the first paper demonstrating the feasibility of single cell transcriptomics with, the number of cells one could assay is also increasing […]

Paper Summary: Fast and accurate single-cell RNA-seq analysis using equivalence class counts




One of the most common applications of single-cell RNA-seq data is to use it to characterize the heterogeneity of  cell populations and identify new cell types or sub-populations.  Typically one uses single-cell RNA-sequencing (RNA-seq) data, quantify gene expression on all cells and use the common gene-expression profile among the cells to characterize the cell-to-cell heterogeneity by […]

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, […]

Interesting papers from the GTEx (Genotype-Tissue Expression) Project




It has been a good week for RNA-seq enthusiasts. First, Kallisto, a new way to quantify transcript expression, happened at BOG15. And this weeks’ Science magazine has three interesting papers on the GTEx (Genotype-Tissue Expression) Project, dealing with boatload of RNA-seq data, a whopping 1641 human RNA-seq samples to be precise. In  addition, there are three […]