RNA-seq analysis
RNAdetector- New Tool for RNA-Seq Data Analysis

In this article, we discuss a new tool that is developed for RNA-Seq data analysis. A new tool called RNAdetector [1] is developed for RNA-Seq data analysis.
RNAdetector is a user-friendly stand-alone tool and a cloud-based platform that helps in RNA-Seq data analysis. It provides an easy-to-use graphical user interface that helps in analyzing coding and non-coding RNAs from RNA datasets.
RNAdetector is a comprehensive pipeline that allows mRNAs and ncRNAs analysis including several classes of humans, C.elegans, and mice [1]. They are stored in a remote repository of RNAdetector that can be easily downloaded from the user interface. Besides, users can perform downstream analysis and miRNA-sensitive topological pathway analysis.
RNAdetector is available as a Docker container for its easy installation. It is cross-platform and requires input files such as FASTQ, SAM, or BAM files. RNAdetector is freely available to download from https://rnadetector.atlas.dmi.unict.it/download.html. The source code is available on GitHub and the documentation can be found at https://github.com/alessandrolaferlita/RNAdetector/wiki/Requirements-and-Setup.
For more details, read here.
References
- La Ferlita, A., Alaimo, S., Di Bella, S. et al. (2021). RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinformatics 22, 298.
RNA-seq analysis
Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
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. (more…)
RNA-seq analysis
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. (more…)
RNA-seq analysis
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]. (more…)
RNA-seq analysis
Most widely used web servers/software for single-cell RNA-seq analysis

Gene expression in single cells is measured using single-cell RNA sequencing technology. It helps in finding new and available cell types of different tissues and organs. In this article, the most widely used web servers and software for single-cell RNA-seq analysis are discussed. (more…)
You must be logged in to post a comment Login