Genome Visualization

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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

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