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Date: Friday, March 28, 2025
Time: 11:01 PM - 11:01 PM EDT
Location: Web Conference (See WebEx information below)
Speakers:
Dr. Bill Wysocki, Director of User Services, University of Chicago (UChicago)
Dr. Zhenyu Zhang, GDC Co-Principal Investigator, University of Chicago (UChicago)
Intended Audience

This webinar is designed for cancer researchers and bioinformaticians who are interested in exploring the latest updates to the NCI Genomic Data Commons (GDC) whole genome sequencing workflows for variant calling.

Abstract

The GDC processes and provides access to diverse genomic data types, including whole genome sequencing (WGS), to identify genetic variants such as SNPs, indels, and structural variations across coding, non-coding, and regulatory regions. The GDC WGS variant calling workflows produce various downstream data types, including simple somatic mutations (SSMs), structural variants (SVs), and copy number variations (CNVs). These workflows utilize advanced tools like Mutect2, SvABA, Strelka, Manta, and GATK4 CNV. In this webinar, the GDC will present the latest updates to GDC WGS variant calling workflows.

Included Topics
  • An overview of the GDC WGS variant calling workflows and latest updates
  • A demonstration of how to access and download WGS variant call data
  • Guidance on locating documentation and Docker files for GDC WGS workflows
Webex Information

GDC WGS Variant Calling Workflow Updates

  • Monday, March 31, 2025
  • 2:00 pm    |    Eastern Standard Time (New York, GMT-04:00)    |    1 hr
  • Meeting number (access code): 2307 201 1512
  • Meeting password: i2dXeT3c6u$ (42393832 when dialing from a phone or video system)

REGISTER/JOIN WEBEX MEETING.

IMPORTANT NOTICE: Please note that this Webex service allows audio and other information sent during the session to be recorded, which may be discoverable in a legal matter. By joining this session, you automatically consent to such recordings. If you do not consent to being recorded, discuss your concerns with the host or do not join the session.

Why do some genes show no expression in STAR results across all samples, even though I can see mapped reads in the raw RNA-Seq data?

Submitted by gaheens on

STAR gene expression quantification excludes reads that are mapped to multiple different genes. This can cause some genes to appear with zero expression in the final counts, even if mapped reads are present in the raw data. 

Date: Friday, March 28, 2025
Time: 11:01 PM - 11:01 PM EDT
Location: Web Conference (See WebEx information below)
Speakers:
Dr. Bill Wysocki, Director of User Services, University of Chicago (UChicago)
Dr. Xin Zhou, Assistant Member, St. Jude Children's Research Hospital

The Sequence Reads and BAM Slicing tools, available in GDC 2.0, are powerful web-based resources for analyzing sequence reads. The Sequence Reads Tool enables users to visualize read alignments from BAM files, and classify reads supporting either the reference or alternative alleles based on variant information (e.g., chromosome, position, reference, and alternative alleles). The BAM Slicing Tool allows users to download specific sections of a BAM file, targeting particular genomic or unmapped regions, thus avoiding the need to download large, multi-gigabyte files. This webinar provides a comprehensive overview of both tools.


Intended Audience

This webinar is designed for researchers interested in visualizing DNA or RNA sequencing reads or downloading Binary Alignment Map (BAM) slices for a specific gene, position, SNP, or variant. It is ideal for anyone looking to analyze sequence reads for cancer mutations, regardless of their prior experience in genomics.

Abstract

The Sequence Reads and BAM Slicing tools, available in GDC 2.0, are powerful web-based resources for analyzing sequence reads. The Sequence Reads Tool enables users to visualize read alignments from BAM files, and classify reads supporting either the reference or alternative alleles based on variant information (e.g., chromosome, position, reference, and alternative alleles). The BAM Slicing Tool allows users to download specific sections of a BAM file, targeting particular genomic or unmapped regions, thus avoiding the need to download large, multi-gigabyte files. This webinar will provide a comprehensive overview of both tools.

For additional details, please see the Sequence Reads Analysis with GDC 2.0 Webinar Presentation.

Included Topics
  • How to utilize the Sequence Reads Tool to visualize sequence reads for a specific gene, position, SNP, or variant 
  • How to download BAM slices for a given gene, position, SNP, or variant using the BAM Slicing Tool 
  • Live Q&A session to address user questions and gather feedback
Webex Information

Sequence Reads Analysis with GDC 2.0: Exploring the Sequence Reads and BAM Slicing Tools

  • Monday, November 18, 2024
  • 2:00 pm    |    Eastern Standard Time (New York, GMT-04:00)    |    1 hr
  • Meeting number (access code): 2308 983 1043
  • Meeting password: yjTQygA@475 (95879421 when dialing from a phone or video system)

REGISTER/JOIN WEBEX MEETING.

IMPORTANT NOTICE: Please note that this Webex service allows audio and other information sent during the session to be recorded, which may be discoverable in a legal matter. By joining this session, you automatically consent to such recordings. If you do not consent to being recorded, discuss your concerns with the host or do not join the session.

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