Tag Archives: data analysis pipeline

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RNA-Seq with iReport and InSilico DB

RNA-Seq with iReport and InSilico DB

RNA-Seq, or transcriptome sequencing, continues to be an exciting way to explore gene expression using next-generation sequencing (NGS). But for many researchers, the interpretation of RNA-Seq data remains a daunting task because they are using spreadsheets to read transcript names ...

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Pipeline for Large RNA-Seq Projects

Pipeline for Large RNA-Seq Projects

Steve Searle from the Sanger Institute talks about the pipeline for large RNA-seq projects. This workshop was filmed during a recent event, Computational Challenges and Performance Optimizations in NGS Data Analyses, jointly organized by Intel and the Francis Crick Institute. ...

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Tutorial – RNA-Seq output to quantification of differential gene expression

Next-generation RNA-sequencing (RNA-Seq) is rapidly outcompeting microarrays as the technology of choice for whole-transcriptome studies. However, the bioinformatics skills required for RNA-Seq data analysis often pose a significant hurdle for many biologists. Here, researchers at Utrecht University, The Netherlands put forward ...

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OmicScript pipeline for RNA-Seq data analysis

ArrayStudio is a GUI software in Windows. OmicSoft also provides a command line tool (named Oshell). Oshell.exe is a .NET application, and it has also been optimized in the Linux environment using the MONO application. In this article, I will ...

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MMAPPR – Mutation Mapping Analysis Pipeline for Pooled RNA-seq

Forward genetic screens in model organisms are vital for identifying novel genes essential for developmental or disease processes. One drawback of these screens is the labor-intensive and sometimes inconclusive process of mapping the causative mutation. In order to leverage high-throughput ...

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Technical considerations for functional sequencing assays

RNA-Seq The measurement of RNA expression is a foundation of many experiments done in biomedical research. It is therefore natural that the sequencing of long and short RNA both for quantification and discovery is the most popular functional sequencing assay ...

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RNA-Seq Data Analysis – Where To Start?

In our last reader poll, we asked: Do we yet have a firm handle on the most appropriate/accurate pipeline for analysis of RNA-Seq datasets? The overwhelming result was: NO. N=72 We’re hearing feedback now from scientists developing data analysis methods ...

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