Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic...
Read More »Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets
Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and...
Read More »Mitochondrial RNA editing – complex transcript repertoires revealed with a dedicated mapping tool
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3′ to ...
Read More »Discover hidden splicing variations by mapping personal transcriptomes to personal genomes
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site ...
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 Bioinformatics – New RNA-Seq Protocols from Methods in Molecular Biology
RNA Bioinformatics Edited by Ernesto Picardi ISBN: 978-1-4939-2290-1 (Print) 978-1-4939-2291-8 (Online) Analysis of High-Throughput RNA Sequencing Data Quality Control of RNA-Seq Experiments Xing Li, Asha Nair, Shengqin Wang, Liguo Wang Pages 137-146 Accurate Mapping of RNA-Seq Data Kin Fai Au ...
Read More »Workshop Materials – mRNA-Seq at Michigan State University
This is the material for two workshops given at MSU by Titus Brown and Matt Scholz. The first workshop (Dec 4/5) was on model organism mRNAseq, and the second workshop (Dec 10/11) will be on semi-model organism mRNAseq. Both workshops ...
Read More »Rcount – simple and flexible RNA-Seq read counting
Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with ...
Read More »RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs
Small non-coding RNAs represent RNA species that are not translated to proteins, but which have diverse and broad functional activities in physiological and pathophysiological states. The knowledge of these small RNAs is rapidly expanding in part through the use of ...
Read More »Application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes
Researchers at the Academy of Sciences of the Czech Republic propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. ...
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