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QCBio Research Seminar: Giovanni Quinones Valdez (Xiao), Grad student in Bioengineering

October 27 @ 12:00 pm - 12:30 pm

TITLE: “scAllele, a versatile tool for the detection and analysis of variants in scRNA-seq.”

ABSTRACT: Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. The read-specific variant calls by scAllele enables allele-specific splicing analysis. Applied to a lung cancer scRNA-seq data set, scAllele identified variants with strong allelic linkage to alternative splicing, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data.

 

Details

Date:
October 27
Time:
12:00 pm - 12:30 pm
Event Category:

Venue

ZOOM
CA United States
Website:
ucla.zoom.us

Organizer

QCBio

Details

Date:
October 27
Time:
12:00 pm - 12:30 pm
Event Category:

Venue

ZOOM
CA United States
Website:
ucla.zoom.us

Organizer

QCBio