Genome Visualization
Channel: Bioinformatics DotCa
Date: 2018-05-25

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