Mercurial > repos > iuc > dada2_makesequencetable
diff topics/metagenomics/tutorials/dada2/tutorial.md @ 4:1c9b3bcd4261 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author | iuc |
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date | Mon, 01 Feb 2021 20:25:05 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/topics/metagenomics/tutorials/dada2/tutorial.md Mon Feb 01 20:25:05 2021 +0000 @@ -0,0 +1,642 @@ +--- +layout: tutorial_hands_on + +title: 16S Microbial Analysis with mothur (extended) +zenodo_link: https://doi.org/10.5281/zenodo.800651 +questions: +- What is the effect of normal variation in the gut microbiome on host health? +objectives: +- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy +- Using a mock community to assess the error rate of your sequencing experiment +- Visualize sample diversity using Krona and Phinch +time_estimation: '' +key_points: +- 16S rRNA gene sequencing analysis results depend on the many algorithms used and + their settings +- Quality control and cleaning of your data is a crucial step in order to obtain optimal + results +- Adding a mock community to serve as a control sample can help you asses the error + rate of your experimental setup +- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations +contributors: +- shiltemann +- bebatut +- tnabtaf + +--- + + +# Introduction +{:.no_toc} + +<!-- This is a comment. --> + +General introduction about the topic and then an introduction of the +tutorial (the questions and the objectives). It is nice also to have a +scheme to sum up the pipeline used during the tutorial. The idea is to +give to trainees insight into the content of the tutorial and the (theoretical +and technical) key concepts they will learn. + +You may want to cite some publications; this can be done by adding citations to the +bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations +must be in bibtex format. If you have the DOI for the paper you wish to cite, you can +get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org). + +With the example you will find in the `tutorial.bib` file, you can add a citation to +this article here in your tutorial like this: +{% raw %} `{% cite Batut2018 %}`{% endraw %}. +This will be rendered like this: {% cite Batut2018 %}, and links to a +[bibliography section](#bibliography) which will automatically be created at the end of the +tutorial. + + +**Please follow our +[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)** + +> ### Agenda +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Title for your first section + +Give some background about what the trainees will be doing in the section. +Remember that many people reading your materials will likely be novices, +so make sure to explain all the relevant concepts. + +## Title for a subsection +Section and subsection titles will be displayed in the tutorial index on the left side of +the page, so try to make them informative and concise! + +# Hands-on Sections +Below are a series of hand-on boxes, one for each tool in your workflow file. +Often you may wish to combine several boxes into one or make other adjustments such +as breaking the tutorial into sections, we encourage you to make such changes as you +see fit, this is just a starting point :) + +Anywhere you find the word "***TODO***", there is something that needs to be changed +depending on the specifics of your tutorial. + +have fun! + +## Get data + +> ### {% icon hands_on %} Hands-on: Data upload +> +> 1. Create a new history for this tutorial +> 2. Import the files from [Zenodo]() or from the shared data library +> +> ``` +> +> ``` +> ***TODO***: *Add the files by the ones on Zenodo here (if not added)* +> +> ***TODO***: *Remove the useless files (if added)* +> +> {% include snippets/import_via_link.md %} +> {% include snippets/import_from_data_library.md %} +> +> 3. Rename the datasets +> 4. Check that the datatype +> +> {% include snippets/change_datatype.md datatype="datatypes" %} +> +> 5. Add to each database a tag corresponding to ... +> +> {% include snippets/add_tag.md %} +> +{: .hands_on} + +# Title of the section usually corresponding to a big step in the analysis + +It comes first a description of the step: some background and some theory. +Some image can be added there to support the theory explanation: + +![Alternative text](../../images/image_name "Legend of the image") + +The idea is to keep the theory description before quite simple to focus more on the practical part. + +***TODO***: *Consider adding a detail box to expand the theory* + +> ### {% icon details %} More details about the theory +> +> But to describe more details, it is possible to use the detail boxes which are expandable +> +{: .details} + +A big step can have several subsections or sub steps: + + +## Sub-step with **dada2_plotComplexity** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotQualityProfile** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_filterAndTrim** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotComplexity** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_plotQualityProfile** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **Unzip Collection** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **Unzip Collection** {% icon tool %} with the following parameters: +> - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %}) +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_learnErrors** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_learnErrors** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_learnErrors** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_dada** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_dada** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_dada** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_dada** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_mergePairs** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_mergePairs** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_makeSequenceTable** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_removeBimeraDenovo** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_seqCounts** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_seqCounts** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + +## Sub-step with **dada2_assignTaxonomyAddspecies** + +> ### {% icon hands_on %} Hands-on: Task description +> +> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters: +> +> ***TODO***: *Check parameter descriptions* +> +> ***TODO***: *Consider adding a comment or tip box* +> +> > ### {% icon comment %} Comment +> > +> > A comment about the tool or something else. This box can also be in the main text +> {: .comment} +> +{: .hands_on} + +***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* + +> ### {% icon question %} Questions +> +> 1. Question1? +> 2. Question2? +> +> > ### {% icon solution %} Solution +> > +> > 1. Answer for question1 +> > 2. Answer for question2 +> > +> {: .solution} +> +{: .question} + + +## Re-arrange + +To create the template, each step of the workflow had its own subsection. + +***TODO***: *Re-arrange the generated subsections into sections or other subsections. +Consider merging some hands-on boxes to have a meaningful flow of the analyses* + +# Conclusion +{:.no_toc} + +Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the +pipeline used. \ No newline at end of file