Many applications of multiple sequence alignments (MSA) involve working with sequences which are not ideal – they can be incomplete, contain errors or just be highly divergent with many mismatches. This is very common when working with high throughput sequencing ...
Read More »An RNA sequencing workflow to characterize the tumor microenvironment
RNA sequencing (RNA-seq) is an integral tool in immunogenomics, allowing for interrogation of the transcriptome of a tumor and its microenvironment. Analytical methods to deconstruct the genomics data can then be applied to infer gene expression...
Read More »Limitation of alignment-free tools in total RNA-seq quantification
Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify...
Read More »Evaluation of tools for long read RNA-seq splice-aware alignment
High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens ...
Read More »Comprehensive benchmarking of RNA-Seq aligners
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. Researchers from the University of ...
Read More »An RNA-Seq QC Overview
Quality control (QC) is a critical step in RNA sequencing (RNA-seq). Yet, it is often ignored or conducted on a limited basis. Here, Vanderbilt University researchers present a multi-perspective strategy for QC of RNA-seq experiments. The QC of RNA-seq can ...
Read More »Commonly used RNA-seq alignment and variant calling programs perform poorly in detecting intermediate long indels (>2 bases) that are clinically actionable
Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly ...
Read More »RapMap – Unreasonably Fast and Accurate Transcriptome Mapping
from RoBlog by Rob Patro – Thoughts and musings on science and life Introducing RapMap I’ve recently been working with my student Avi Srivastava on a new project, RapMap. RapMap is a tool for mapping (see below for the distinction between mapping ...
Read More »RNA-Seq Alignment and Visualization
Canadian Bioinformatics Workshops – Informatics for RNA-sequence Analysis (QC) (2014) – Module 2 – RNA-seq alignment and visualization High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq ...
Read More »CADBURE – A generic tool to evaluate the performance of spliced aligners on RNA-Seq data
The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for ...
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