Monthly Archives: June 2010

Ensembl Update (e58) with RNA-Seq Data

Zebrafish RNASeq models (Zebrafish) A new set of gene models made using RNA-Seq data from 9 tissues. The gene set has exon and transcript level RPKM values for each tissue stored as supporting features. The models are an additional gene ...

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MapPER – A New Tool for Aligning Paired-end RNA-seq Data

A Probabilistic Framework for Aligning Paired-end RNA-seq Data Motivation: The RNA-seq paired-end read (PER) protocol samples transcript fragments longer than the sequencing capability of today’s technology by sequencing just the two ends of each fragment. Deep sampling of the transcriptome ...

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Featured Review Articles – Transcriptomics

Transcriptomics: Throwing light on dark matter Louisa Flintoft Nature Reviews Genetics 11, 455-455 (July 2010) Transcriptomics: Common disease pathogenesis pathways Gemma K. Alderton Nature Reviews Genetics 11, 386-386 (June 2010) Transcriptomics: a further step in the right direction. Boscolo-Berto R. ...

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rQuant.web: a tool for RNA-Seq-based transcript quantitation

A novel web service, called rQuant.web, allows convenient access to tools for quantitative analysis of RNA sequencing data. The underlying quantitation technique rQuant is based on quadratic programming and estimates different biases induced by library preparation, sequencing and read mapping. It ...

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RNA-Seq Data Analysis Tools

Scripture – is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. Cufflinks – assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq ...

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Featured Publication – Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation1, 2, 3. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in ...

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RNA-Seq Technical Guide

from Genome Web RNA-seq, though, is a fairly new approach and investigators are still working out all the kinks. So that’s what we focus on in this installment of Genome Technology‘s technical guide series. In these pages, our panel of ...

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