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Date: Tuesday, April 29, 2025
Time: 4:04 AM - 4:04 AM 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)
Dr. Xin Zhou, Assistant Member, St. Jude Children's Research Hospital
Intended Audience

This webinar is designed for researchers interested in learning how the GDC harmonizes single cell RNA-Seq data and provides an overview of the new GDC Single Cell RNA-Seq Tool which visualizes single-cell RNA-Seq data with cluster plots and gene expression overlays. It is ideal for anyone looking to analyze single cell RNA-Seq data for cancer research, regardless of their prior experience in genomics.

Abstract

The GDC processes single-cell RNA-Seq (scRNA-Seq) data using the Cell Ranger pipeline to calculate gene expression, followed by Seurat for secondary expression analysis, and makes the aligned reads file (BAM), as well as raw and filtered counts (MEX) accessible to the research community. Researchers can analyze scRNA-Seq data using the newly developed GDC scRNA-Seq Tool, which streamlines the exploration of single cell RNA sequencing data through cluster plots and gene expression overlays. The tool supports dimensionality reduction visualization using UMAP, tSNE, and PCA plots, facilitates the analysis of gene expression patterns across clusters, and enables differential expression and Gene Set Enrichment Analysis (GSEA). Additionally, it allows researchers to examine gene expression distributions across clusters and perform pairwise comparisons with descriptive statistics. Expression data can also be accessed programmatically using the new GDC scRNA-Seq gene expression API endpoint. This webinar will provide an in-depth look at GDC scRNA-Seq workflows, demonstrate how the scRNA-Seq Tool can enhance single-cell research efforts, and review the GDC scRNA-Seq gene expression API.

Included Topics
  • Overview of GDC workflows for harmonizing single cell RNA-Seq data 
  • Demonstration of the GDC Single Cell RNA-Seq tool 
  • Review of the GDC Single Cell gene expression API for programmatic access 
  • Live Q&A session to address user questions and gather feedback
Webex Information

GDC Single Cell RNA-Seq Analysis

  • Monday, May 19, 2025
  • 2:00 pm    |    Eastern Standard Time (New York, GMT-04:00)    |    1 hr
  • Meeting number (access code): 2304 934 2573
  • Meeting password: sS6c8W55uh* (77628955 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.

Date: Tuesday, April 29, 2025
Time: 4:04 AM - 4:04 AM 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. 

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