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 […]

HISAT2 for aligning reads against human population

HISAT2, the next iteration of HISAT – the splice-aware low memory alignment program by Daehwan Kim from Steven Salzberg’s team is out. Actually, the beta version of HISAT2 has been available since September, but somehow missed it until HISAT2 was presented as talk at #GI2015. HISAT2 is not just the next iteration of HISAT, HISAT2 can do […]

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, […]