SMS scnews item created by Dario Strbenac at Wed 26 May 2021 1000
Type: Seminar
Distribution: World
Expiry: 30 Jun 2021
Calendar1: 31 May 2021 1300-1330
CalLoc1: Zoom videoconferencing
Auth: dario@ (dstr7320) in SMS-SAML

Statistical Bioinformatics Webinar: Su -- Visualising Nanopore Methylation Data with NanoMethViz

Presented by Mr.  Shian Su, Walter and Eliza Hall Institute 

Signals produced by Oxford Nanopore direct DNA sequencing contains information that can
be used to infer DNA modifications, providing an effective new tool for high-throughput
and high-resolution analysis of genome-wide DNA methylation patterns.  Our focus is on
5-methylcytosine CpG DNA methylation, which plays an essential role in the epigenetic
regulation of mammalian gene expression.  We produced a dataset of long read DNA
sequencing on F1 cross female placenta data from known parental strains to demonstrate
the utility of nanopore sequencing for investigating methylation.  The
well-characterised parental strains and long read sequences allow us to haplotype a
majority of reads, and placental tissue guarantees paternal X-inactivation.  We
developed a package NanoMethViz to process and visualise the results from this data.
NanoMethViz standardises data from multiple popular methylation callers and produces
plots of methylation patterns at varying resolutions from sample overview to individual
reads.  We explore the patterns of methylation within imprinted and x-inactivated genes,
as well as repeat elements.

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