MAY 13, 2015 10:30 AM PDT

Transcriptome Assembly: Computational Challenges of Next-Generation Sequence Data

Speaker
  • Director, Center for Computational Biology McKusick-Nathans Institute of Genetic Medicine, Professor, Departments of Biomedical Engineering, Computer Science, and Biostatistics
    BIOGRAPHY

Abstract

Next-generation sequencing technology allows us to peer inside the cell in exquisite detail, revealing new insights into biology, evolution, and disease that would have been impossible to discover just a few years ago. The enormous volumes of data produced by NGS experiments present many computational challenges that we are working to address. One of the most widely used sequencing methods is RNA-seq, which captures the genes being transcribed in a cell and uses sequencing to measure their levels of expression. In recent years, my lab has developed multiple systems for RNA-seq analysis, including the widely-used Bowtie, TopHat and Cufflinks programs for alignment and assembly of transcripts from RNA-seq data. In this presentation, I will describe two new systems, each of which represents a major step forward: (1) the HISAT system for spliced aligment of NGS reads, a successor to TopHat; and (2) the StringTie program for assembly and quantitation of RNA-seq data, a successor to Cufflinks. This talk describes joint work with Daehwan Kim and Mihaela Pertea. Learning Objectives: 1. Explain the overall process used to turn RNA sequence data into a summary of genes and their expression levels 2. Describe why it is difficult to align a short RNA or DNA sequence to the human genome 3. Appreciate the computational challenge of assembling a complete, correct set of transcripts from a large next-generation sequencing experiment.


Show Resources
You May Also Like
SEP 14, 2021 7:00 AM PDT
C.E. CREDITS
SEP 14, 2021 7:00 AM PDT
Date: September 14, 2021 Time: 7am PDT, 10am EDT, 4pm CEST A conventional thermal cycler has long been a commodity product in the lab and end-point PCR techniques can be completed almost wit...
MAY 11, 2021 10:00 AM PDT
C.E. CREDITS
MAY 11, 2021 10:00 AM PDT
Date: May 11, 2021 Time: 10:00zm PDT Your samples are some of the most valuable assets in the laboratory. After spending countless hours on extraction and preparation, your conclusions could...
FEB 24, 2021 10:00 AM PST
C.E. CREDITS
FEB 24, 2021 10:00 AM PST
DATE: February 24, 2021 TIME: 10am PST Automated lab instruments such as liquid handlers and cell sorters are increasingly common in all types of laboratories, driving fast results for labor...
MAR 18, 2021 8:00 AM PDT
C.E. CREDITS
MAR 18, 2021 8:00 AM PDT
DATE: March 18, 2021 TIME: 8:00am PDT Sequencing of bulk cells, single cells, and nuclei is opening doors in the understanding of complex biological processes....
JUL 15, 2021 9:00 AM PDT
JUL 15, 2021 9:00 AM PDT
Date: July 15, 2021 Time: 9:00am (PDT), 12:00pm (EDT) The Pisces workflow robust, easy-to-use, end-to-end multi-omics solution for highly multiplexed targeted Spatial RNA analysis. VeranomeB...
JUN 08, 2021 9:00 AM PDT
JUN 08, 2021 9:00 AM PDT
Date: June 8, 2021 Time: 9:00am PDT Reducing the spread of highly infectious and deadly diseases within the population, vaccine development is crucial in saving millions of lives each year....
MAY 13, 2015 10:30 AM PDT

Transcriptome Assembly: Computational Challenges of Next-Generation Sequence Data


Specialty

Antibodies

Virology

Immunology

Dna Sequencing

Personalized Medicine

Clinical Diagnostics

Immunity

Cancer Diagnostics

Immunotherapy

Bioinformatics

Flow Cytometry

Immuno-Oncology

Gene Expression

Dna

Big Data

Geography

Europe100%

Registration Source

Website Visitors100%

Job Title

Student100%

Organization

Academic Institution100%


Show Resources
Loading Comments...
Show Resources