Advances in transcriptome sequencing (RNA-Seq) have revolutionized the way to characterize and quantify transcripts. The breakthroughs in RNA-Seq technologies give rise to the ever-increasing volumes of data, making data processing the bottleneck of transcriptome research. It becomes crucial to develop ...
Read More »TCGA_RNASeq_Clinical – Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas
The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides “Le3” data, which have been processed using a pipeline specific to that resource. However, researchers from the University of Utah have found using experimentally derived data ...
Read More »DeTCT – a purely quantitative digital gene expression sample processing and analysis package
Many RNA-seq methods are excellent tools for in-depth mRNA expression analysis of small numbers of samples and provide information on the entire RNA molecule, alternative splicing and the quantity of transcript. However, they require an involved library preparation and often ...
Read More »Featured RNA-Seq Job – Sequence Pipeline Developer
University of California – San Francisco (San Francisco, CA) Req Number – 42709BR Job Title – Sequence Pipeline Developer Job Code and Payroll Title – 7275 PROGRAMMER/ANALYST III Location – Mission Bay Department Name – Psychiatry Work Days – Monday ...
Read More »Running a pipeline of modules for analyzing RNA-Seq data in GenePattern
In this video step, we will run a previously constructed GenePattern pipeline for analyzing RNA-Seq data. Our pipeline is named RNA_exp. To run it, we start from the pipeline run-page which lists the necessary input files just like a module ...
Read More »RNAMiner – A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable ...
Read More »TRUP- Identification of novel fusion genes using breakpoint assembly of RNA-Seq data
Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. A team led by researchers at the University of ...
Read More »Omics Pipe: A Community-based Framework for Reproducible Multi-Omics Data Analysis
Omics Pipe is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of ...
Read More »TIGAR2 – estimation of transcript isoform expression with longer RNA-Seq reads
High-throughput RNA sequencing (RNA-Seq) enables quantification and identification of transcripts at single-base resolution. Recently, longer sequence reads become available thanks to the development of new types of sequencing technologies as well as improvements in chemical reagents for the Next Generation ...
Read More »Workshop Materials – mRNA-Seq at Michigan State University
This is the material for two workshops given at MSU by Titus Brown and Matt Scholz. The first workshop (Dec 4/5) was on model organism mRNAseq, and the second workshop (Dec 10/11) will be on semi-model organism mRNAseq. Both workshops ...
Read More »