RNA-seq analysis

Installing TopHat2 on Ubuntu


TopHat is one of the most widely used tools for RNA-seq reads to map splice junction [1]. It uses Bowtie to align mammalian genomes. The older versions of TopHat require the separate installation of SAMTools. But the versions 2.0 onwards come with an inbuilt stable SAMTools package. In this article, we will install TopHat2.1.1. on Ubuntu. Keep Reading

RNAIndel: A tool to identify somatic indels from tumor RNA-seq data


It is a challenging task to discover somatic coding indels that are generated during the preparation of the PCR-based RNA-seq library. A new tool called RNAIndel [1] has been developed for this purpose. Keep Reading

Differential Gene Expression Analysis of RNA-Seq data using MeV


Differential gene expression analysis helps in discovering quantitative changes in the expression levels between the experimental groups. For that, statistical testing is done using various software. In this article, we will analyze RNA seq count data using the edgeR module present in the Multiple Experiment Viewer (MeV) [1,2]. Keep Reading

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