Mercurial > repos > iuc > dada2_mergepairs
comparison topics/metagenomics/tutorials/dada2/tutorial.md @ 4:306a40d4bb8f 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 20:22:27 +0000 |
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1 --- | |
2 layout: tutorial_hands_on | |
3 | |
4 title: 16S Microbial Analysis with mothur (extended) | |
5 zenodo_link: https://doi.org/10.5281/zenodo.800651 | |
6 questions: | |
7 - What is the effect of normal variation in the gut microbiome on host health? | |
8 objectives: | |
9 - Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy | |
10 - Using a mock community to assess the error rate of your sequencing experiment | |
11 - Visualize sample diversity using Krona and Phinch | |
12 time_estimation: '' | |
13 key_points: | |
14 - 16S rRNA gene sequencing analysis results depend on the many algorithms used and | |
15 their settings | |
16 - Quality control and cleaning of your data is a crucial step in order to obtain optimal | |
17 results | |
18 - Adding a mock community to serve as a control sample can help you asses the error | |
19 rate of your experimental setup | |
20 - We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations | |
21 contributors: | |
22 - shiltemann | |
23 - bebatut | |
24 - tnabtaf | |
25 | |
26 --- | |
27 | |
28 | |
29 # Introduction | |
30 {:.no_toc} | |
31 | |
32 <!-- This is a comment. --> | |
33 | |
34 General introduction about the topic and then an introduction of the | |
35 tutorial (the questions and the objectives). It is nice also to have a | |
36 scheme to sum up the pipeline used during the tutorial. The idea is to | |
37 give to trainees insight into the content of the tutorial and the (theoretical | |
38 and technical) key concepts they will learn. | |
39 | |
40 You may want to cite some publications; this can be done by adding citations to the | |
41 bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations | |
42 must be in bibtex format. If you have the DOI for the paper you wish to cite, you can | |
43 get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org). | |
44 | |
45 With the example you will find in the `tutorial.bib` file, you can add a citation to | |
46 this article here in your tutorial like this: | |
47 {% raw %} `{% cite Batut2018 %}`{% endraw %}. | |
48 This will be rendered like this: {% cite Batut2018 %}, and links to a | |
49 [bibliography section](#bibliography) which will automatically be created at the end of the | |
50 tutorial. | |
51 | |
52 | |
53 **Please follow our | |
54 [tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)** | |
55 | |
56 > ### Agenda | |
57 > | |
58 > In this tutorial, we will cover: | |
59 > | |
60 > 1. TOC | |
61 > {:toc} | |
62 > | |
63 {: .agenda} | |
64 | |
65 # Title for your first section | |
66 | |
67 Give some background about what the trainees will be doing in the section. | |
68 Remember that many people reading your materials will likely be novices, | |
69 so make sure to explain all the relevant concepts. | |
70 | |
71 ## Title for a subsection | |
72 Section and subsection titles will be displayed in the tutorial index on the left side of | |
73 the page, so try to make them informative and concise! | |
74 | |
75 # Hands-on Sections | |
76 Below are a series of hand-on boxes, one for each tool in your workflow file. | |
77 Often you may wish to combine several boxes into one or make other adjustments such | |
78 as breaking the tutorial into sections, we encourage you to make such changes as you | |
79 see fit, this is just a starting point :) | |
80 | |
81 Anywhere you find the word "***TODO***", there is something that needs to be changed | |
82 depending on the specifics of your tutorial. | |
83 | |
84 have fun! | |
85 | |
86 ## Get data | |
87 | |
88 > ### {% icon hands_on %} Hands-on: Data upload | |
89 > | |
90 > 1. Create a new history for this tutorial | |
91 > 2. Import the files from [Zenodo]() or from the shared data library | |
92 > | |
93 > ``` | |
94 > | |
95 > ``` | |
96 > ***TODO***: *Add the files by the ones on Zenodo here (if not added)* | |
97 > | |
98 > ***TODO***: *Remove the useless files (if added)* | |
99 > | |
100 > {% include snippets/import_via_link.md %} | |
101 > {% include snippets/import_from_data_library.md %} | |
102 > | |
103 > 3. Rename the datasets | |
104 > 4. Check that the datatype | |
105 > | |
106 > {% include snippets/change_datatype.md datatype="datatypes" %} | |
107 > | |
108 > 5. Add to each database a tag corresponding to ... | |
109 > | |
110 > {% include snippets/add_tag.md %} | |
111 > | |
112 {: .hands_on} | |
113 | |
114 # Title of the section usually corresponding to a big step in the analysis | |
115 | |
116 It comes first a description of the step: some background and some theory. | |
117 Some image can be added there to support the theory explanation: | |
118 | |
119 ![Alternative text](../../images/image_name "Legend of the image") | |
120 | |
121 The idea is to keep the theory description before quite simple to focus more on the practical part. | |
122 | |
123 ***TODO***: *Consider adding a detail box to expand the theory* | |
124 | |
125 > ### {% icon details %} More details about the theory | |
126 > | |
127 > But to describe more details, it is possible to use the detail boxes which are expandable | |
128 > | |
129 {: .details} | |
130 | |
131 A big step can have several subsections or sub steps: | |
132 | |
133 | |
134 ## Sub-step with **dada2_plotComplexity** | |
135 | |
136 > ### {% icon hands_on %} Hands-on: Task description | |
137 > | |
138 > 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: | |
139 > | |
140 > ***TODO***: *Check parameter descriptions* | |
141 > | |
142 > ***TODO***: *Consider adding a comment or tip box* | |
143 > | |
144 > > ### {% icon comment %} Comment | |
145 > > | |
146 > > A comment about the tool or something else. This box can also be in the main text | |
147 > {: .comment} | |
148 > | |
149 {: .hands_on} | |
150 | |
151 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
152 | |
153 > ### {% icon question %} Questions | |
154 > | |
155 > 1. Question1? | |
156 > 2. Question2? | |
157 > | |
158 > > ### {% icon solution %} Solution | |
159 > > | |
160 > > 1. Answer for question1 | |
161 > > 2. Answer for question2 | |
162 > > | |
163 > {: .solution} | |
164 > | |
165 {: .question} | |
166 | |
167 ## Sub-step with **dada2_plotQualityProfile** | |
168 | |
169 > ### {% icon hands_on %} Hands-on: Task description | |
170 > | |
171 > 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: | |
172 > | |
173 > ***TODO***: *Check parameter descriptions* | |
174 > | |
175 > ***TODO***: *Consider adding a comment or tip box* | |
176 > | |
177 > > ### {% icon comment %} Comment | |
178 > > | |
179 > > A comment about the tool or something else. This box can also be in the main text | |
180 > {: .comment} | |
181 > | |
182 {: .hands_on} | |
183 | |
184 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
185 | |
186 > ### {% icon question %} Questions | |
187 > | |
188 > 1. Question1? | |
189 > 2. Question2? | |
190 > | |
191 > > ### {% icon solution %} Solution | |
192 > > | |
193 > > 1. Answer for question1 | |
194 > > 2. Answer for question2 | |
195 > > | |
196 > {: .solution} | |
197 > | |
198 {: .question} | |
199 | |
200 ## Sub-step with **dada2_filterAndTrim** | |
201 | |
202 > ### {% icon hands_on %} Hands-on: Task description | |
203 > | |
204 > 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters: | |
205 > | |
206 > ***TODO***: *Check parameter descriptions* | |
207 > | |
208 > ***TODO***: *Consider adding a comment or tip box* | |
209 > | |
210 > > ### {% icon comment %} Comment | |
211 > > | |
212 > > A comment about the tool or something else. This box can also be in the main text | |
213 > {: .comment} | |
214 > | |
215 {: .hands_on} | |
216 | |
217 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
218 | |
219 > ### {% icon question %} Questions | |
220 > | |
221 > 1. Question1? | |
222 > 2. Question2? | |
223 > | |
224 > > ### {% icon solution %} Solution | |
225 > > | |
226 > > 1. Answer for question1 | |
227 > > 2. Answer for question2 | |
228 > > | |
229 > {: .solution} | |
230 > | |
231 {: .question} | |
232 | |
233 ## Sub-step with **dada2_plotComplexity** | |
234 | |
235 > ### {% icon hands_on %} Hands-on: Task description | |
236 > | |
237 > 1. **dada2_plotComplexity** {% icon tool %} with the following parameters: | |
238 > | |
239 > ***TODO***: *Check parameter descriptions* | |
240 > | |
241 > ***TODO***: *Consider adding a comment or tip box* | |
242 > | |
243 > > ### {% icon comment %} Comment | |
244 > > | |
245 > > A comment about the tool or something else. This box can also be in the main text | |
246 > {: .comment} | |
247 > | |
248 {: .hands_on} | |
249 | |
250 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
251 | |
252 > ### {% icon question %} Questions | |
253 > | |
254 > 1. Question1? | |
255 > 2. Question2? | |
256 > | |
257 > > ### {% icon solution %} Solution | |
258 > > | |
259 > > 1. Answer for question1 | |
260 > > 2. Answer for question2 | |
261 > > | |
262 > {: .solution} | |
263 > | |
264 {: .question} | |
265 | |
266 ## Sub-step with **dada2_plotQualityProfile** | |
267 | |
268 > ### {% icon hands_on %} Hands-on: Task description | |
269 > | |
270 > 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters: | |
271 > | |
272 > ***TODO***: *Check parameter descriptions* | |
273 > | |
274 > ***TODO***: *Consider adding a comment or tip box* | |
275 > | |
276 > > ### {% icon comment %} Comment | |
277 > > | |
278 > > A comment about the tool or something else. This box can also be in the main text | |
279 > {: .comment} | |
280 > | |
281 {: .hands_on} | |
282 | |
283 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
284 | |
285 > ### {% icon question %} Questions | |
286 > | |
287 > 1. Question1? | |
288 > 2. Question2? | |
289 > | |
290 > > ### {% icon solution %} Solution | |
291 > > | |
292 > > 1. Answer for question1 | |
293 > > 2. Answer for question2 | |
294 > > | |
295 > {: .solution} | |
296 > | |
297 {: .question} | |
298 | |
299 ## Sub-step with **Unzip Collection** | |
300 | |
301 > ### {% icon hands_on %} Hands-on: Task description | |
302 > | |
303 > 1. **Unzip Collection** {% icon tool %} with the following parameters: | |
304 > - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %}) | |
305 > | |
306 > ***TODO***: *Check parameter descriptions* | |
307 > | |
308 > ***TODO***: *Consider adding a comment or tip box* | |
309 > | |
310 > > ### {% icon comment %} Comment | |
311 > > | |
312 > > A comment about the tool or something else. This box can also be in the main text | |
313 > {: .comment} | |
314 > | |
315 {: .hands_on} | |
316 | |
317 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
318 | |
319 > ### {% icon question %} Questions | |
320 > | |
321 > 1. Question1? | |
322 > 2. Question2? | |
323 > | |
324 > > ### {% icon solution %} Solution | |
325 > > | |
326 > > 1. Answer for question1 | |
327 > > 2. Answer for question2 | |
328 > > | |
329 > {: .solution} | |
330 > | |
331 {: .question} | |
332 | |
333 ## Sub-step with **dada2_learnErrors** | |
334 | |
335 > ### {% icon hands_on %} Hands-on: Task description | |
336 > | |
337 > 1. **dada2_learnErrors** {% icon tool %} with the following parameters: | |
338 > | |
339 > ***TODO***: *Check parameter descriptions* | |
340 > | |
341 > ***TODO***: *Consider adding a comment or tip box* | |
342 > | |
343 > > ### {% icon comment %} Comment | |
344 > > | |
345 > > A comment about the tool or something else. This box can also be in the main text | |
346 > {: .comment} | |
347 > | |
348 {: .hands_on} | |
349 | |
350 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
351 | |
352 > ### {% icon question %} Questions | |
353 > | |
354 > 1. Question1? | |
355 > 2. Question2? | |
356 > | |
357 > > ### {% icon solution %} Solution | |
358 > > | |
359 > > 1. Answer for question1 | |
360 > > 2. Answer for question2 | |
361 > > | |
362 > {: .solution} | |
363 > | |
364 {: .question} | |
365 | |
366 ## Sub-step with **dada2_learnErrors** | |
367 | |
368 > ### {% icon hands_on %} Hands-on: Task description | |
369 > | |
370 > 1. **dada2_learnErrors** {% icon tool %} with the following parameters: | |
371 > | |
372 > ***TODO***: *Check parameter descriptions* | |
373 > | |
374 > ***TODO***: *Consider adding a comment or tip box* | |
375 > | |
376 > > ### {% icon comment %} Comment | |
377 > > | |
378 > > A comment about the tool or something else. This box can also be in the main text | |
379 > {: .comment} | |
380 > | |
381 {: .hands_on} | |
382 | |
383 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
384 | |
385 > ### {% icon question %} Questions | |
386 > | |
387 > 1. Question1? | |
388 > 2. Question2? | |
389 > | |
390 > > ### {% icon solution %} Solution | |
391 > > | |
392 > > 1. Answer for question1 | |
393 > > 2. Answer for question2 | |
394 > > | |
395 > {: .solution} | |
396 > | |
397 {: .question} | |
398 | |
399 ## Sub-step with **dada2_dada** | |
400 | |
401 > ### {% icon hands_on %} Hands-on: Task description | |
402 > | |
403 > 1. **dada2_dada** {% icon tool %} with the following parameters: | |
404 > | |
405 > ***TODO***: *Check parameter descriptions* | |
406 > | |
407 > ***TODO***: *Consider adding a comment or tip box* | |
408 > | |
409 > > ### {% icon comment %} Comment | |
410 > > | |
411 > > A comment about the tool or something else. This box can also be in the main text | |
412 > {: .comment} | |
413 > | |
414 {: .hands_on} | |
415 | |
416 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
417 | |
418 > ### {% icon question %} Questions | |
419 > | |
420 > 1. Question1? | |
421 > 2. Question2? | |
422 > | |
423 > > ### {% icon solution %} Solution | |
424 > > | |
425 > > 1. Answer for question1 | |
426 > > 2. Answer for question2 | |
427 > > | |
428 > {: .solution} | |
429 > | |
430 {: .question} | |
431 | |
432 ## Sub-step with **dada2_dada** | |
433 | |
434 > ### {% icon hands_on %} Hands-on: Task description | |
435 > | |
436 > 1. **dada2_dada** {% icon tool %} with the following parameters: | |
437 > | |
438 > ***TODO***: *Check parameter descriptions* | |
439 > | |
440 > ***TODO***: *Consider adding a comment or tip box* | |
441 > | |
442 > > ### {% icon comment %} Comment | |
443 > > | |
444 > > A comment about the tool or something else. This box can also be in the main text | |
445 > {: .comment} | |
446 > | |
447 {: .hands_on} | |
448 | |
449 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
450 | |
451 > ### {% icon question %} Questions | |
452 > | |
453 > 1. Question1? | |
454 > 2. Question2? | |
455 > | |
456 > > ### {% icon solution %} Solution | |
457 > > | |
458 > > 1. Answer for question1 | |
459 > > 2. Answer for question2 | |
460 > > | |
461 > {: .solution} | |
462 > | |
463 {: .question} | |
464 | |
465 ## Sub-step with **dada2_mergePairs** | |
466 | |
467 > ### {% icon hands_on %} Hands-on: Task description | |
468 > | |
469 > 1. **dada2_mergePairs** {% icon tool %} with the following parameters: | |
470 > | |
471 > ***TODO***: *Check parameter descriptions* | |
472 > | |
473 > ***TODO***: *Consider adding a comment or tip box* | |
474 > | |
475 > > ### {% icon comment %} Comment | |
476 > > | |
477 > > A comment about the tool or something else. This box can also be in the main text | |
478 > {: .comment} | |
479 > | |
480 {: .hands_on} | |
481 | |
482 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
483 | |
484 > ### {% icon question %} Questions | |
485 > | |
486 > 1. Question1? | |
487 > 2. Question2? | |
488 > | |
489 > > ### {% icon solution %} Solution | |
490 > > | |
491 > > 1. Answer for question1 | |
492 > > 2. Answer for question2 | |
493 > > | |
494 > {: .solution} | |
495 > | |
496 {: .question} | |
497 | |
498 ## Sub-step with **dada2_makeSequenceTable** | |
499 | |
500 > ### {% icon hands_on %} Hands-on: Task description | |
501 > | |
502 > 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters: | |
503 > | |
504 > ***TODO***: *Check parameter descriptions* | |
505 > | |
506 > ***TODO***: *Consider adding a comment or tip box* | |
507 > | |
508 > > ### {% icon comment %} Comment | |
509 > > | |
510 > > A comment about the tool or something else. This box can also be in the main text | |
511 > {: .comment} | |
512 > | |
513 {: .hands_on} | |
514 | |
515 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
516 | |
517 > ### {% icon question %} Questions | |
518 > | |
519 > 1. Question1? | |
520 > 2. Question2? | |
521 > | |
522 > > ### {% icon solution %} Solution | |
523 > > | |
524 > > 1. Answer for question1 | |
525 > > 2. Answer for question2 | |
526 > > | |
527 > {: .solution} | |
528 > | |
529 {: .question} | |
530 | |
531 ## Sub-step with **dada2_removeBimeraDenovo** | |
532 | |
533 > ### {% icon hands_on %} Hands-on: Task description | |
534 > | |
535 > 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters: | |
536 > | |
537 > ***TODO***: *Check parameter descriptions* | |
538 > | |
539 > ***TODO***: *Consider adding a comment or tip box* | |
540 > | |
541 > > ### {% icon comment %} Comment | |
542 > > | |
543 > > A comment about the tool or something else. This box can also be in the main text | |
544 > {: .comment} | |
545 > | |
546 {: .hands_on} | |
547 | |
548 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
549 | |
550 > ### {% icon question %} Questions | |
551 > | |
552 > 1. Question1? | |
553 > 2. Question2? | |
554 > | |
555 > > ### {% icon solution %} Solution | |
556 > > | |
557 > > 1. Answer for question1 | |
558 > > 2. Answer for question2 | |
559 > > | |
560 > {: .solution} | |
561 > | |
562 {: .question} | |
563 | |
564 ## Sub-step with **dada2_seqCounts** | |
565 | |
566 > ### {% icon hands_on %} Hands-on: Task description | |
567 > | |
568 > 1. **dada2_seqCounts** {% icon tool %} with the following parameters: | |
569 > | |
570 > ***TODO***: *Check parameter descriptions* | |
571 > | |
572 > ***TODO***: *Consider adding a comment or tip box* | |
573 > | |
574 > > ### {% icon comment %} Comment | |
575 > > | |
576 > > A comment about the tool or something else. This box can also be in the main text | |
577 > {: .comment} | |
578 > | |
579 {: .hands_on} | |
580 | |
581 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
582 | |
583 > ### {% icon question %} Questions | |
584 > | |
585 > 1. Question1? | |
586 > 2. Question2? | |
587 > | |
588 > > ### {% icon solution %} Solution | |
589 > > | |
590 > > 1. Answer for question1 | |
591 > > 2. Answer for question2 | |
592 > > | |
593 > {: .solution} | |
594 > | |
595 {: .question} | |
596 | |
597 ## Sub-step with **dada2_assignTaxonomyAddspecies** | |
598 | |
599 > ### {% icon hands_on %} Hands-on: Task description | |
600 > | |
601 > 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters: | |
602 > | |
603 > ***TODO***: *Check parameter descriptions* | |
604 > | |
605 > ***TODO***: *Consider adding a comment or tip box* | |
606 > | |
607 > > ### {% icon comment %} Comment | |
608 > > | |
609 > > A comment about the tool or something else. This box can also be in the main text | |
610 > {: .comment} | |
611 > | |
612 {: .hands_on} | |
613 | |
614 ***TODO***: *Consider adding a question to test the learners understanding of the previous exercise* | |
615 | |
616 > ### {% icon question %} Questions | |
617 > | |
618 > 1. Question1? | |
619 > 2. Question2? | |
620 > | |
621 > > ### {% icon solution %} Solution | |
622 > > | |
623 > > 1. Answer for question1 | |
624 > > 2. Answer for question2 | |
625 > > | |
626 > {: .solution} | |
627 > | |
628 {: .question} | |
629 | |
630 | |
631 ## Re-arrange | |
632 | |
633 To create the template, each step of the workflow had its own subsection. | |
634 | |
635 ***TODO***: *Re-arrange the generated subsections into sections or other subsections. | |
636 Consider merging some hands-on boxes to have a meaningful flow of the analyses* | |
637 | |
638 # Conclusion | |
639 {:.no_toc} | |
640 | |
641 Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the | |
642 pipeline used. |