Tag Archives: pipeline

An increasing body of evidence suggests an important role of the human microbiome in health and disease. Researchers at UCLA have developed a ‘lost and found’ pipeline, which examines high quality unmapped sequence reads for microbial taxonomic classification. Using this ...

Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data. Researchers at the University ...

Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance ...

This presentation was filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. For more information and to view other videos from the March 2015 GATK Workshop, please visit the GATK Workshop page.

RNA sequencing (RNA-seq) has revolutionized transcriptome analysis through profiling the expression of thousands of genes at the same time. Systematic analysis of orthologous transcripts across species is critical for understanding the evolution of gene expression and uncovering important information in ...

A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to ...

Small non-coding RNAs have been significantly recognized as the key modulators in many biological processes, and are emerging as promising biomarkers for several diseases. These RNA species are transcribed in cells and can be packaged in extracellular vesicles, which are ...

Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted ...

Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives ...

Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the ...