Analysis Pipelines

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omiRas – A MicroRNA-Seq Data Analysis Pipeline

omiRas – A MicroRNA-Seq Data Analysis Pipeline

To identify circulating miRNA biomarkers for AD, researchers from Meiji Pharmaceutical University, Japan reanalyzed a publicly available small RNA-Seq dataset, composed of blood samples derived from 48 AD patients and 22 normal control (NC) subjects, by a simple web-based miRNA ...

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New microRNA Analysis App in BaseSpace

New microRNA Analysis App in BaseSpace

miRNAs are a class of non-coding RNAs mainly involved in post-transcription control of gene expression although they are also involved in other non-canonical functions. Furthermore, they represents an interesting class of biomarkers for a large variety of diseases. Small RNA-sequencing ...

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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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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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