Topics – GATK
Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data Need Help? Search our documentation Community Forum Hi, How can we help? Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capabl
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression an
RNA-Seq Workshop
Do you want to learn the basics of how to analyze RNA-Seq data, including genome-based and genome-free transcript reconstruction and differential expression analysis? Below, we provide materials to help get you started. A VirtualBox virtual machine image is provided that includes several popular tools for analyzing RNA-Seq, including Tuxedo for genome-based and Trinity for genome-free RNA-Seq stud
GC-Content Normalization for RNA-Seq Data | RNA-Seq Blog
Transcriptome sequencing (RNA-Seq) has become the assay of choice for high-throughput studies of gene expression. However, as is the case with microarrays, major technology-related artifacts and biases affect the resulting expression measures. Normalization is therefore essential to ensure accurate inference of expression levels and subsequent analyses thereof. A group led by researchers at Univer
NuGEN - Ovation® RNA-Seq System V2
Next-Gen Sequencing Ovation® RNA-Seq FFPE System Ovation® WGA FFPE System Ovation® RNA-Seq V2 Ovation® RNA-Seq Ovation® 3'-DGE System Ovation® Ultralow Library Systems Encore™ Complete RNA-Seq Library Systems Encore™ Library for Ion Torrent Encore™ Library System I Encore™ Multiplex System I Encore™ NGS Multiplex System IB Encore™ 384 Multiplex System Encore™ Library Spike-in Controls
RNA-seq: Finding Differentially Expressed Genes
Here are some notes on processing RNA-seq data to find differentially expressed genes. A much abbreviated version of this pipeline comes from Cufflink’s Tutorial Page The extended version given below follows the more exploratory pattern of someone who hasn’t done much (any) NGS data analysis before. Tools Used TopHat v1.1.2 Cufflinks v1.0.1 Samtools v0.1.16 Requirements Sequence Files We are start
Allele-specific gene expression by RNA-seq | RNA-Seq Blog
Variation in gene expression is thought to make a significant contribution to phenotypic diversity among individuals within populations. Although high-throughput cDNA sequencing offers a unique opportunity to delineate the genome-wide architecture of regulatory variation, new statistical methods need to be developed to capitalize on the wealth of information contained in RNA-seq data sets. Researc
Browse Articles | Nature Reviews Genetics
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Improving genetic diagnosis in Mendelian disease with transcriptome sequencing – a walk through
(Modern, mid-2016) RNA-seq software pipeline
Using Kallisto for expression analysis of published RNAseq data | Bench to Bioinformatics
Methods to Study Splicing from RNA-Seq
Real-time streaming differential RNA-seq analysis with eXpress
Differential Gene Expression heatmap from RNA-Seq data using cummeRbund | InSilico DB Genomic Datasets Hub
http://www.genomeweb.com/node/1050091?hq_e=el&hq_m=1246296&hq_l=5&hq_v=9290c016b0
Galaxy
Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA
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