ngs_intro_workshop

Introductory workshop on analysis of NGS data in Galaxy and other online tools

• Intro
• Variants
• RNA-Seq

Plan for delivery

Session 1 - General NGS

Dataset TBC

Intro and Experimental Design

13:00 - 13:30

Galaxy Introduction

13:30 - 14:00

Upload some fastq files

14:00 - 14:30

fastqc

14:30 - 15:00

multiqc

15:00 - 15:15

alignment - bwa

15:15 - 15:30

the bam file

15:30 - 15:45

marking duplicates?

15:45 - 16:00

IGV Introduction

16:00 - 16:30

Session 2 - Variant Calling

Create new History and Upload files

13:00 - 13:15

Align to reference

13:15 - 13:30

Load bams into IGV and inspect

13:30 - 14:00

Initial variant calling with freebayes

14:00 - 14:30

VCF Filtering

14:45 - 15:00

VCF Intersecting

15:00 - 15:15

Annotation

15:15 - 15:30

Cancer Genomes

Upload the data and align

Variant call with varscan

annotation with wAnnovar

Copy Number

SV calling