2017-ucsc-metagenomics
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2017 Metagenomics workshop at UC Santa Cruz
Welcome!
Booting a Jetstream Computer Instance for your use!
Short read quality and trimming
Run the MEGAHIT assembler
Annotation with Prokka
Mapping and Binning a Metagenome Assembly
Gene Abundance Estimation with Salmon
Mapping
Slicing and dicing with k-mers
Using and Installing Circos
Workflow and repeatability discussion
Data
Building this site on your own
2017 / April / Metagenomics
Day 2 - installation instructions
K-mer Spectral Error Trimming
Page
Table of Contents
2017 Metageno... »
Source
Table of Contents
ΒΆ
Tutorials:
2017 Metagenomics workshop at UC Santa Cruz
Day 1: Noon to 5pm
Day 2: Morning (9am - noon)
Day 2: Afternoon (1:15pm - 5pm)
Undone
Technical information
Welcome!
1. Learning goals
2. Safe space and code of conduct
3. Instructor introductions
4. Jetstream and cloud computing - why?!
5. Sticky notes and how they work... + Minute Cards
Booting a Jetstream Computer Instance for your use!
Request to log in to the Jetstream Portal
Use “XSEDE”
Fill in the username and password and click “Sign in”
Select Projects and “Create New Project”
Name the project for yourself, click “create”
Select the newly created project
Within the project, select “new”
Find the “Ubuntu 14.04.3” image, click on it
Name it something simple and select ‘m1.medium’
Wait for it to become active
Click on your new instance to get more information!
Short read quality and trimming
Installing some software
Running Jupyter Notebook
Data source
1. Copying in some data to work with.
1. Copying data into a working location
2. FastQC
3. Trimmomatic
4. FastQC again
Run the MEGAHIT assembler
While the assembly runs...
After the assembly is finished
Annotation with Prokka
Installing Prokka
Running Prokka
Questions?
References
Mapping and Binning a Metagenome Assembly
Mapping
Binning
Gene Abundance Estimation with Salmon
Installing Salmon
Running Salmon
Working with count data
Plotting the results
References
Mapping
Downloading data
Mapping the reads
Converting to BAM to visualize
Visualizing the read mapping
Slicing and dicing with k-mers
Assemble the slice
Using and Installing Circos
Installing Circos
Visualizing Gene Coverage and Orientation
References
Workflow and repeatability discussion
Data
Building this site on your own
2017 / April / Metagenomics
Day 2 - installation instructions
Running Jupyter Notebook
K-mer Spectral Error Trimming
Why (or why not) do k-mer trimming?
LICENSE:
This documentation and all textual/graphic site content is released under
Creative Commons - 0 (CC0)
--
fork @ github
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