Tag Archives: read mapping

Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while ...

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all ...

In recent years, the massively-parallel cDNA sequencing (RNA-Seq) technologies have become a powerful tool to provide high resolution measurement of expression and high sensitivity in detecting low abundance transcripts. However, RNA-seq data requires a huge amount of computational efforts. The ...

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most ...

The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in the de novo setting or when a trusted reference ...

RNA-SEQ – Mapping to a Reference Genome – by Kevin Libuit

Dr. Robine, New York Genome Center, lectures on “Understanding RNA-Seq analysis”

This presentation was filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. For more information and to view other videos from the March 2015 GATK Workshop, please visit the GATK Workshop page.

As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering ...

Date: February 10th-12th, 2016 Location: Room PC95 (first floor), RADIX building (107), Wageningen Campus, Droevendaalsesteeg 1, Wageningen, the Netherlands Directions: directions (check also Map Wageningen UR Campus) Language: English Group size: maximum of 35 participants Credits: 0.8 ECTS Registration and ...