Analysis of Metagenomic Data: Metatranscriptomics

This is the sixth module in the 2016 Analysis of Metagenomic Data workshop hosted by the Canadian Bioinformatics Workshops. This lecture is by John Parkinson from SickKids.

How it Begins by Kevin MacLeod is licensed under a Creative Commons Attribution license (https://creativecommons.org/licenses/...)
Source: http://incompetech.com/music/royalty-...
Artist: http://incompetech.com/

Table of Contents:

00:10 -
00:22 - Learning Objectives of Module
01:26 - Overview
02:44 - Metagenomics and metatranscriptomics reveal function
05:38 -
07:32 - Similar microbiomes can express different functions
10:00 -
18:24 - A typical metatranscriptomic analytical pipeline
20:35 - 1. Sample collection and RNA extraction
28:30 - A typical metatranscriptomic analytical pipeline
28:31 -
28:32 - Similar microbiomes can express different functions
28:57 -
29:00 - A typical metatranscriptomic analytical pipeline
29:01 - 1. Sample collection and RNA extraction
32:10 - 2. Preparing sample for sequencing
36:26 - 2. Preparing sample for sequencing
38:26 - 3. Generating reads
39:49 - 4. Analysing the data
42:46 - Read processing - filtering
43:46 - Read processing - Assembly
46:03 - Read processing – functional annotation
48:51 - Read processing – functional annotation
51:26 - Quality of BLASTX matches
52:27 - Read processing – converting mappings to expression
53:50 - Read processing – taxonomic annotation
54:55 - Read processing – taxonomic annotation
56:23 - Taxonomic assignment through Gist
56:47 - GIST exploits several orthogonal methods to define genome signatures
56:57 - Assigning genome specific weights for each method
57:36 - Gist performance against a mouse metatranscriptome
59:05 - mRNA expression is not equivalent to rRNA abundance
59:54 - Visualizing results
01:00:50 - Visualizing results
01:01:58 - Visualizing results
01:03:36 - Visualizing results
01:04:49 - Visualizing results
01:06:27 - Visualizing results
01:07:34 - Visualizing results
01:08:58 - Statistical considerations
01:11:06 - Statistical considerations
01:12:16 -