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RNA-Seq Data Preprocessing Tutorial

RNA-Seq Data Preprocessing Tutorial

Check the full description for links to all the resources and the protocol etc. This tutorial follows the Delhomme et al. Epigenesys protocol for RNA sequencing data preprocessing in order to finally perform a differential expression study. To demonstrate, we ...

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Genome-wide profiling of the C. elegans dsRNAome

Genome-wide profiling of the C. elegans dsRNAome

Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, researchers at the ...

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The impact of quality filter for RNA-Seq

The impact of quality filter for RNA-Seq

With the emergence of large-scale sequencing platforms since 2005, there has been a great revolution regarding methods for decoding DNA sequences, which have also affected quantitative and qualitative gene expression analyses through the RNA-Sequencing technique. However, issues related to the ...

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A comparative study of RNA-seq analysis strategies

A comparative study of RNA-seq analysis strategies

Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a ...

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Scrimer – designing primers from transcriptome data

Scrimer – designing primers from transcriptome data

With the rise of next-generation sequencing methods it has become increasingly possible to obtain genome-wide sequence data even for non-model species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which can subsequently be screened ...

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RNA-Seq Analysis – Using Tophat & Cufflinks

RNA-Seq Analysis – Using Tophat & Cufflinks

Yan Kou – Ma’ayan Lab – Icahn School of Medicine – Introduction to Big Data analysis in systems biology including statistical methods used to identify differentially expressed genes, performing various types of enrichment analyses, and applying clustering algorithms.

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