Tag Archives: pipeline

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...