While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events...
Read More »ESFinder – Identification of Exon Skipping Events from High-Throughput RNA Sequencing Data
The emergence of next-generation high-throughput RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate identification of alternative splicing events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) ...
Read More »SplAdder – Identification, quantification and testing of alternative splicing events from RNA-Seq data
Understanding the occurrence and regulation of alternative splicing (AS) is a key task towards explaining the regulatory processes that help to shape the complex transcriptomes of higher eukaryotes. With the advent of high-throughput sequencing of RNA, the diversity of AS ...
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 »AStalavista – Analysis of Alternative Splicing Events in Custom Gene Datasets
Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process is highly regulated and makes up a ...
Read More »SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq
High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Now, a team led by researchers at the ...
Read More »51% of non-canonical splice sites are not annotated in GENCODE
Scientists at the Pontifical Catholic University of Chile have uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. They mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent ...
Read More »KisSplice – de novo Assembly of Alternative Splicing Events from RNA-seq Data
Gustavo Sacomoto In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each ...
Read More »Transcriptome analysis of alternative splicing events
Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, researchers at the Chinese Academy of Sciences used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. They found ...
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