Monthly Archives: June 2011

SeqGene – general purpose software for mining post-aligment RNA-Seq datasets

SeqGene is an open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, allele specific expression, and expression-genotying association analysis. SeqGene is especially suited for RNA-seq and exonome-seq applications, ...

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RNA-Seq News – from GenomeWeb

Variability Across RNA-seq Experiments Suggests Need for Careful Study Design Researchers found that even at high coverage, the estimate of the relative abundance of a particular transcript can “substantially disagree” between sequencing experiments using the same platforms and protocols. Study ...

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FlyBase adds RNA-Seq Data Sets

FlyBase has just incorporated several new RNA-Seq data sets from the modENCODE project. These data sets differ from our current RNA-Seq data in that the expression is displayed by strand. One of these data sets includes temporal expression data from ...

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Genome Annotation with RNA-Seq

While RNA-Seq’s capability of high-resolution and accuracy in transcript abundance estimation has been thoroughly demonstrated, (so much so that it is being heralded as a possible replacement for microarray based gene expression technology) there is another important application for RNA-Seq; ...

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Moving Next-Gen Sequencing into the Clinic

The FDA has begun to develop their program to evaluate sequencing based diagnostics. At a recent meeting, the Association for Molecular Pathology (AMP) advised FDA officials on many important considerations for evaluating the analytical validity of next-generation sequencing: The analytical ...

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Advanced RNA-Seq Course

Date:                  Aug 25-26, 2011 Location:         Amsterdam Medical Centre, Amsterdam Organizer:       NBIC & LUMC Contact(s):      Dr. Celia van Gelder Level:               PhD NBIC and LUMC will organize a 2-day course on RNA-seq data analysis on August 25 and 26, ...

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Beginner RNA-Seq Data Analysis Pipeline

If you’re new to RNA-Seq or computational Biology in general, here is a short presentation overview. from Wei Sun – Assistant professor, University of North Carolina-Chapel Hill Department of Biostatistics – Bios 784: Introduction to Computational Biology – class notes ...

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