Update:

• Nowlan Freese and Ann Loraine made edits yesterday in-office
• decided to submit abstracts today after another look in the morning, using fresh eyes

Submitted abstracts:

Title #1: Visual analysis of RNA-Seq data in the Integrated Genome Browser; why every researcher needs to view their data
Abstract #1:
Next-generation RNA sequencing (RNA-Seq) is a widely used and powerful method for detecting gene expression and understanding gene function. RNA-Seq data processing pipelines involve many steps, with many parameter choices along the way. Producing and processing RNA-Seq data requires diligent quality control to catch or avoid mistakes. One of the best ways to avoid mistakes is to visually examine the RNA-Seq alignments in a genome browser. To make visual inspection of RNA-Seq alignments more effective and convenient, we added several new features to Integrated Genome Browser (IGB), an open-source, highly interactive and customizable computational tool users can download and install from the BioViz project website. Here, we demonstrate how to use these IGB features to identify problems in RNA-Seq data arising from experimental or data processing errors. Examples to be presented include: visualizing soft-clipped reads in an RNA-Seq experiment where the reads failed to split across introns, layering data from multiple replicates to identify point mutations that indicate sample switching at a sequencing facility, and viewing RNA-Seq data where the intron length parameter was not set correctly, leading to chromosome-spanning introns. By documenting instances where visualization in a genome browser helps expose and ultimately correct mistakes, we hope to convince researchers that genomic visualization is essential to a successful RNA-Seq experiment.

Title #2: Upcoming version of Integrated Genome Browser will better support visualizing and exploring personal genome sequence data
Abstract #2:
Direct-to-consumer genomic sequencing services are relatively inexpensive now, making them accessible for families and individuals to explore the health and ancestry implications of their own personal genomes. To help personal genome sequencing clients better understand their own data, we added new capabilities to the Integrated Genome Browser (IGB), a freely available open-source desktop genome browser that supports fast navigation through vast data scenes. IGB supports layering multiple data sources onto an annotated reference genome. It includes customizable “LinkOuts” to external Web sites, enabling users to easily navigate to external data sources with information about genes and polymorphisms. As of upcoming IGB version 10.1.0, IGB will be able to display genome sequence data imported from Compressed Reference-oriented Alignment Map (CRAM) files, used by genome sequencing providers to distribute data. Because IGB runs locally, CRAM files can reside on a user’s personal computer, without requiring prior upload to a server or website. We also developed an IGB App for formatting of SNP array data for display. By comparing whole-genome sequencing to SNP array data, users can better understand and sanity-check results.

Both abstracts have been submitted to the 2024 ASHG conference. The submission information and receipts can be found in:
Dropbox / IGB / Outreach / Conferences / 2024-ASHG

Closing ticket.

Dear Paige Kulzer:

This confirms that your abstract (2024-A-4091-ASHG Upcoming version of Integrated Genome Browser will better support visualizing and exploring personal genome sequence data) has been ACCEPTED for a poster presentation at the 2024 American Society of Human Genetics Annual Meeting in Denver, CO, from November 5-9.