Genome Visualization

This is the second module of the Informatics on High Throughput Sequencing Data 2018 workshop hosted by the Canadian Bioinformatics Workshops at the Ontario Institute for Cancer Research. This session is by Hamza Farooq from the University of Toronto and Sick Kids Research Institute. Table of Contents: 00:16 - Learning Objectives of Module 00:58 - Organization 01:24 - 01:27 - 01:49 - Anscombe’s quartet 02:15 - Anscombe’s quartet 03:02 - The Datasaurus Dozen 03:41 - Preattentive vs attentive visual processing 04:21 - Preattentive attributes 04:43 - Why visualize? 05:18 - Visualization tools in genomics 05:50 - HT-seq Genome Browsers 06:38 - Integrative Genomics Viewer (IGV) 06:54 - Integrative Genomics Viewer (IGV) 07:28 - Features 08:12 - IGV data sources 08:36 - Using IGV: the basics 08:57 - Launch IGV 09:33 - Launch IGV 10:08 - Load data 10:49 - Screen layout 10:55 - Screen layout 12:12 - Screen layout 12:13 - Load data 12:26 - Screen layout 12:27 - Screen layout 12:46 - File formats and track types 13:31 - Viewing alignments 13:55 - Viewing alignments – Zoom in 14:56 - Viewing alignments – Zoom in 16:04 - SNVs and Structural variations 16:50 - Viewing alignments – Zoom in 17:12 - SNVs and Structural variations 17:37 - Viewing SNPs and SNVs 18:36 - Viewing SNPs and SNVs 19:08 - Viewing SNPs and SNVs 19:44 - Viewing SNPs and SNVs 19:45 - Viewing Structural Events 19:46 - Viewing SNPs and SNVs 19:51 - Viewing Structural Events 20:14 - Paired-end sequencing 20:37 - Paired-end sequencing 20:47 - Paired-end sequencing 21:09 - Interpreting inferred insert size 21:32 - Deletion 21:38 - Deletion 21:49 - Deletion 21:56 - Deletion 22:11 - Deletion 22:28 - Color by insert size 22:34 - Deletion 23:00 - Insert size color scheme 23:32 - Rearrangement 23:47 - Rearrangement 24:00 - Rearrangement 24:01 - Insert size color scheme 24:05 - Rearrangement 24:06 - Rearrangement 24:13 - Rearrangement 24:14 - Insert size color scheme 26:23 - Rearrangement 26:24 - Rearrangement 26:24 - Interpreting Read-Pair Orientations 27:02 - Inversion 27:06 - Inversion 27:10 - Inversion 27:16 - Inversion 27:23 - Inversion 27:28 - Inversion 27:32 - Inversion 27:36 - Inversion 27:38 - Inversion 27:41 - Inversion 27:46 - Inversion 27:53 - Inversion 27:59 - Inversion 28:15 - Color by pair orientation 28:20 - Inversion 28:58 - 29:29 - Long Read Considerations 30:06 - Long Read Considerations 30:19 - Long Read Considerations 32:06 - Long Read Considerations 32:11 - Long Read Considerations 32:29 - Online Structural Variant Viewers 33:34 - 33:47 - Online Structural Variant Viewers 33:48 - Long Read Considerations 33:48 - Long Read Considerations 33:49 - Long Read Considerations 33:58 - Long Read Considerations 33:58 - Long Read Considerations 33:58 - 33:59 - Inversion 33:59 - Color by pair orientation 34:14 - Inversion 34:15 - 34:15 - Long Read Considerations 34:16 - Long Read Considerations 36:03 - Long Read Considerations 36:04 - 36:04 - Inversion 36:04 - Color by pair orientation 36:05 - Inversion 36:05 - Color by pair orientation 38:07 - Inversion 38:07 - Inversion 38:07 - Inversion 38:09 - Inversion 38:10 - Rearrangement 38:10 - Deletion 38:10 - Deletion 38:11 - Deletion 38:11 - Deletion 38:12 - Deletion