Bioinformatics Training & Education Program

This lesson is part of a course, B4B: Unix and Biowulf.  This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and working with data from a publicly available database (e.g., SRA). 

In Lesson 5: Downloading data from the SRA, attendees will learn how to download data from the Sequence Read Archive. 

Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?  Please join Oxford Nanopore Technologies (ONT) bioinformatics specialists on a deep dive into getting the most from your long read sequencing data.

This workshop will cover the details of analyzing single-cell RNA sequencing data using our EPI2ME pipeline wf-single-cell. This workflow provides access to industry standard tools for primary processing of single-cell data including deconvolution, quality control, gene and transcript identification, and data visualization. Participants will learn about the EPI2ME software, pipeline details, and work with an ONT bioinformatics expert in a hands-on data analysis training exercise.

This in-person, hands-on workshop gives learners the opportunity to learn the Nanopore Single Cell RNA-Seq Analysis Software Workflow. Taught by Nanopore personnel, with assistance from the CCR Genomics Core and BTEP, this session will run in the morning. Space is limited. If your plans change and you cannot attend, please cancel your registration. There will be no hybrid option for this class, it is in-person only. 

Participants should bring an internet-enabled laptop to access the tools and datasets used for the training. 

Agenda:

9:00-9:15 – Check in & distribute materials

9:15-9:30 – Data analysis intro from Oxford Nanopore Technologies (MinKNOW/EPI2ME/other advanced tools)

9:30-10:00 – Introduction to Single Cell RNA-seq data analysis with Oxford Nanopore Technologies

10:00-11:15 – Hands on data analysis: Single Cell EPI2ME App, nextflow command line, and Biowulf HPC demo

11:15-12:00 – Downstream analysis with Seurat

12:00-12:30 – Closing and Q&A

Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?  Please join Oxford Nanopore Technologies (ONT) bioinformatics specialists on a deep dive into getting the most from your long read sequencing data. 

This workshop will cover the details of analyzing human whole genome sequencing data using our EPI2ME pipeline wf-human-variation. This workflow provides users with tools to perform alignment and variant calling for single nucleotide, structural,  and copy number variants as well as clinically relevant short tandem repeats, and cytosine methylation. Participants will learn about the EPI2ME software, pipeline details, and work with an ONT bioinformatics expert in a hands-on data analysis training exercise.

This in-person, hands-on workshop gives learners the opportunity to learn the Nanopore Human Variation Data Analysis Software Workflow. Taught by Nanopore personnel, with assistance from the CCR Genomics Core and BTEP, this session will run in the afternoon. Space is limited. If your plans change and you cannot attend, please cancel your registration. There will be no hybrid option for this class, it is in-person only. 

Participants should bring an internet-enabled laptop to access the tools and datasets used for the training. 

 1:30-1:45 – Check in & distribute materials

1:45-2:15 – Data analysis intro from ONT (MinKNOW/EPI2ME/other advanced tools)

2:15-2:45 – Introduction to the Human Variation (WGS) pipeline

2:45-4:00 – Hands on data analysis: human variation EPI2ME App, nextflow command line, and Biowulf HPC demo

4:00-4:30 – Review result

4:30-5:00 – Closing/Q&A