Tag: Next-gen sequencing

Announcing the first ever RNA-Seq in the Cloud hackathon!

Announcing the first ever RNA-Seq in the Cloud hackathon!

From March 11-13, 2019, the NCBI will help run a bioinformatics hackathon in the North Carolina Research Triangle hosted by the University of North Carolina, Chapel Hill (UNC).

Potential topics include:

  • technical metadata homogenization
  • a simple interface for using ontologies to make data searches more sensitive and specific
  • automated data analysis and visualization
  • novel isoform identification and comparison

We’re looking for people who have experience in working with subjects like these. If this describes you, please apply!

This event is for researchers, including students and postdocs, who use bioinformatics data or develop pipelines for large scale RNA-Seq analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to UNC. Continue reading “Announcing the first ever RNA-Seq in the Cloud hackathon!”

Florida (USF) Biological Data Science “IronHack” February 25-27, 2019

Florida (USF) Biological Data Science “IronHack” February 25-27, 2019

From February 25-27, 2019, NCBI will help with a Data Science hackathon at USF in Tampa Florida!

The hackathon will focus on the genomics of Iron-linked Rare Diseases as well as large scale RNA-Seq indexing and analysis. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to Tampa.

Working groups of five to six individuals will be formed into five to eight teams. These teams will build or expand on pipelines and tools to analyze large datasets within a cloud infrastructure. Example subjects for such hackathons include:

  • Integrative pipelines to analyze large scale RNA-Seq experiments
  • Visualization tools for mapping phenotypes to genotypes
  • Rapid clinical diagnostics tools
  • Structural variant mining with single molecule sequencing data

Please see the application form for more details and additional projects.  The project list will continue to evolve and will be updated on the application form.

Continue reading “Florida (USF) Biological Data Science “IronHack” February 25-27, 2019”

NCBI to assist in Southern California genomics hackathon in January

NCBI to assist in Southern California genomics hackathon in January

From January 10-12, 2018, the NCBI will help with a bioinformatics hackathon in Southern California hosted by San Diego State University. The hackathon will focus on advanced bioinformatics analysis of next generation sequencing data, proteomics, and metadata. This event is for researchers, including students and postdocs, who have already engaged in the use of bioinformatics data or in the development of pipelines for bioinformatics analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).  Applications are due Monday, December 11th, 2017 by 3 pm PT (6PM EST).

Continue reading “NCBI to assist in Southern California genomics hackathon in January”

August 23 NCBI Minute: Using the Run Selector to Find Relevant Next-Generation Sequencing (NGS) Datasets

Do you have trouble searching the NCBI webpage for relevant datasets? Wish you could filter the search results more precisely? You can with SRA Run Selector.

In this NCBI Minute, you’ll learn how to filter the SRA database using the metadata details captured for each submitted dataset. This is easily done in a spreadsheet format that displays all recorded metadata for each SRA Run. The user-friendly interface allows you to selectively filter datasets down to the most relevant data for your research question and then export it in a spreadsheet.

Date and time: Wednesday, August 23, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

The Tasmanian Devil 2: The tumor and Tasmanian devil mitochondrial genomes

The Tasmanian devil (Sarcophilus harrisii), the last remaining large marsupial carnivore, now faces extinction because of a strange and deadly infection, a transmissible cancer known as Transmissible Devil Facial Tumor Disease (TDFTD).  In a previous NCBI Insights post, we discussed gene expression data from the tumors that established their neural origin and showed the tumors were likely derived from Schwann cells.  In this post, we’ll consider some of the genome sequencing projects in the NCBI databases and explore evidence that the tumor originated in a different individual than the affected animal supporting the idea that the tumor cells themselves are infectious agents. Continue reading “The Tasmanian Devil 2: The tumor and Tasmanian devil mitochondrial genomes”

The Human Reference Genome – Understanding the New Genome Assemblies

What is a genome assembly?

The haploid human genome consists of 22 autosomal chromosomes and the Y and the X chromosomes. Each of the chromosomes represents a single DNA molecule, a sequence of millions of nucleotide bases.  These molecules are linear, so one might expect that we should represent each chromosome by a single, continuous sequence.

Unfortunately, this is not the case for two main reasons: 1) because of the nature of genomic DNA and the limitations of our sequencing methods, some parts of the genome remain unsequenced, and 2) emerging evidence suggests that some regions of the genome vary so much between individual people that they cannot be represented as a single sequence.

In response to this, modern genomic data sets present a model of the genome known as a genome assembly. This post will introduce the basic concepts of how we produce such assemblies as well as some basic vocabulary.

Continue reading “The Human Reference Genome – Understanding the New Genome Assemblies”