Create beerDEcoded.yaml #7
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tour/beerDEcoded.yaml
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| id: beerDEcoded | |||
| name: BeerDEcoded - StreetScienceCommunity | |||
| description: BeerDEcoded - StreetScienceCommunity | |||
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Workflow finds yeast strains contained in a sequenced beer sample.
| title_default: <b>BeerDEcoded</b> | ||
| steps: | ||
| - title: <b>BeerDEcoded - StreetScienceCommunity</b> | ||
| content: >- |
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idea maybe the introduction could contain a bit more info about the beer microbiome. Like what microorganisms can be found in a beer. Why are they important. A more general introduction is hopefully already done before and then we could have some repetition issues here.
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I suggest this introduction for the tour:
"Beer contains DNA that comes from its ingredients (hops, malts, yeast) and some hundred microbes. There are 1,000+ yeasts used for brewing and 200+ hop varieties, each one bearing a different DNA and contributing to differentiate its properties.
Thanks for new technologies of sequencing it is easier nowadays to explore the potential of genome sequencing to understand the contribution of various species to product characteristics. The sequencing of the full genome of 157 brewing yeast strains was, for example, recently reported (Gallone B, Steensels J, Prahl T, et al. 2016).
Based on the identification of strains present in beer with desired characteristics, controlled experiments in which the microbial composition of the brew is altered could allow us to investigate if the presence of specific microorganisms affects flavour. The origin of each yeast species can be investigated; i.e. whether they come with the ingredients or from the environment at the production site. Furthermore, plant DNA, such as malt and hop varieties, can be found in beer samples, and the bacterial diversity can be mapped.
"
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In general: sounds very good. Maybe break it up into two boxes, so it is not too much text in one.
Some hints:
- loos the (hops, malts, yeast). In our analysis we only find yeast. Since hops and malts are used early in the brewing process it is very likely that their cells were lysed. The sequencing protocol is not detecting them. To avoid confusion I would delete the (...)
- The sentence 'Thanks for new technologies...' is not clear to me. Maybe say it in easier words: Thanks to sequencing it is now easyer to find the different genomes contained in a beer sample and investigate their characteristics.
- The paper is very interesting. :-)
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In general: sounds very good. Maybe break it up into two boxes, so it is not too much text in one.
Some hints:
- loos the (hops, malts, yeast). In our analysis we only find yeast. Since hops and malts are used early in the brewing process it is very likely that their cells were lysed. The sequencing protocol is not detecting them. To avoid confusion I would delete the (...)
- The sentence 'Thanks for new technologies...' is not clear to me. Maybe say it in easier words: Tanks to sequencing it is now easyer to find the different genomes contained in a beer sample and investigate their characteristics.
- The paper is very interesting. :-)
What if we add also information about 3 steps of the process:
"The beerDeCoded process contains 3 consistent steps. The first step is DNA extraction from beer. Then, this DNA can be sequenced. That means that we can obtain the sequence of nucleotides for this specific DNA. Finally, we have to analyze received data in order to know which organisms this DNA is from." And add the process diagram from https://streetscience.community/projects/beerdecoded/
And point out that we are currently on the third step?
Or this would be redundant information?
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That is a good idea.
In general: It would be good if each box of the tour gets a title, explaining the content of the box. Like this, it will be easy for us to see the flow of the tour.
To this box: It would be good to connect it to the explanation before. E.g. To study the microbiome of beer you need to find out what is inside the beer. Getting this inside can be found by extracting the DNAs of the living organisms (yeast) inside the beer. Now you would also like to 'read' this DNA. This can be achieved by sequencing the DNA.
Having this sequences now enabels us to do a Data analysis, which we will do in the following.
tour/beerDEcoded.yaml
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| intro: Change the name of the new history to <b>'BeerDEcoded'</b>. | ||
| position: left | ||
| - title: <b>Uploading the input data</b> | ||
| content: We need to upload data. We will start with a <b>fastq</b> file. |
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Idea : incorporate a box shortly repainting the structure of a fastq file. Contains reads. One read is stored in 4 lines. What do the lines mean? ... We should have it explained somewhere before I guess, but for this formats, repetition does not harm.
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I suggest to add:
"FASTQ format is a text-based format for storing both a biological sequence and its corresponding quality scores. Both the sequence letter and the quality score are encoded with a single ASCII character for brevity.
A FASTQ file normally uses four lines per sequence.
Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description.
Line 2 is the raw sequence letters.
Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.
You can find more info in the Wikipedia article.
"
tour/beerDEcoded.yaml
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| The upload may take awhile.<br><br> Hit the <b>Close</b> button when you | ||
| see that the files are uploaded into your history. | ||
| - title: <b>Uploading the input data Complete !</b> | ||
| content: 'Now that your data is ready, let''s use some tools.<br>' |
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Idea Now that your data is ready, let's analyze it!
tour/beerDEcoded.yaml
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| - title: <b>Assign taxonomic classifications</b> | ||
| content: >- | ||
| One of the key steps in metagenomic data analysis is to identify the taxon | ||
| to which the individual reads belong. Taxonomic classification tools are |
tour/beerDEcoded.yaml
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| content: >- | ||
| One of the key steps in metagenomic data analysis is to identify the taxon | ||
| to which the individual reads belong. Taxonomic classification tools are | ||
| based on microbial genome databases to identify the origin of each |
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are using microbial ...
done
tour/beerDEcoded.yaml
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| backdrop: true | ||
| - title: <b>Taxonomic classification with Kraken2</b> | ||
| content: >- | ||
| To perform the taxonomic classification we will use Kraken2. This tool |
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Maybe explain the tool in a more simple linguage. Words like: minimizer method k-mers, deterministic, memory, processing time and dustmasker. It could help to draw the tasks or steps of the tool if this is possible.
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I suggest the explanation:
"This tool uses k-mers (the read’s subsequences of length k) to assign a taxonomic label to the sequence (if possible).
The taxonomic label is assigned based on matches of k-mer content of the considering sequence to the k-mer content of reference genome sequence. The result is a classification of the considering sequence to the most likely taxonomic label. If the k-mer content is not similar to any genomic sequence in the database used, it will not assign any taxonomic label.
"
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A figure would be nice. Maybe a pile of readers split in k-mers and then searched in the DB.
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- here I tried to create an approximate figure for simplified description of Kraken2 process
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This looks very nice. Thanks!
| placement: right | ||
| - title: <b>Assign taxonomic labels with Kraken2</b> | ||
| intro: >- | ||
| Please select the following parameters:<br><br> <b>'Single or paired |
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Would be nice to have a short explanation for each or some of the parameters to change. It could be marked as side info, so the games do not have to read them, but if they would like to learn more they can.
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Would be nice to have a short explanation for each or some of the parameters to change. It could be marked as side info, so the games do not have to read them, but if they would like to learn more they can.
I added the info about parameters: Single or paired reads, Confidence and database.
tour/beerDEcoded.yaml
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| element: '#__BVID__106' | ||
| intro: >- | ||
| But before that, we need to adjust the format of the data output from | ||
| Kraken2.<br><br> Search and select the <b>'Reverse'</b> tool. |
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add: It can happen, that the output format of the tool needs to be changed in order for the next tool to read the data. Galaxy offers several "manipulation" tools.
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It could help to explain what format changes should happen, so they understand why they are using the tools.
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add: It can happen, that the output format of the tool needs to be changed in order for the next tool to read the data. Galaxy offers several "manipulation" tools.
done
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It could help to explain what format changes should happen, so they understand why they are using the tools.
I added the info about format changes we need and info about what info kraken2 output contains.
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tour/beerDEcoded.yaml
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| file'</b>: Yes<br> <b>'Format report output like | |||
| Kraken 1’s kraken-mpa-report'</b>: Yes<br> <b>'Select a Kraken2 | |||
| database'</b>: fungi2019-03' <br><br>Click <b>'Next'</b> and the tour will | |||
| <b>'Execute'</b> the Kraken2 tool for you.' | |||
| <b>'Execute'</b> the Kraken2 tool for you.'<br><br><br> | |||
| <small>Additional info:<br><b>Parameter ‘Single or paired reads’</b><br>Single-end reads are the fragments sequenced from one side. With paired-end sequencing, the fragments are sequenced from both sides. This approach results in two reads per fragment, with the first read in forward orientation and the second read in reverse-complement orientation. With this technique, we have the advantage to get more information about each DNA fragment compared to reads sequenced by only single-end sequencing<br><b>Parameter ‘Confidence'</b><br>A confidence score of 0.0 means that non-restrictive taxonomic assignation is desired. This value can be increased if a more restrictive taxonomic assignation is desired. For example, a confidence score of 0.1 means that at least 10% of the k-mers should match entries in the database. <br><b>Parameter ‘Select a Kraken2 database’</b><br>We need to identify the taxon to which the individual reads belong. To identify the origin of each sequence, taxonomic classification tools use microbial genome databases. For this tutorial, we will use the <i>fungi2019-03</i> database.<small/><br> | |||
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I would move Additional info block to the previous step ("Have a look at the tool's parameters of the Kraken2..")
| and Report file.<br><br> It will remain stored in your history.<br><br> | ||
| Click the <b>'eye'</b> icon to view the data once the history item turns | ||
| green. | ||
| position: left |
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I propose to add one additional step with additonal information about Classification file anf Report file format of Kraken2:
"Additional info:
In classification file each sequence (or sequence pair, in the case of paired reads) classified by Kraken 2 results in a single line of output. Kraken 2's output lines contain five tab-delimited fields; from left to right, they are:
- "C"/"U": a one letter code indicating that the sequence was either classified or unclassified.
- The sequence ID, obtained from the FASTA/FASTQ header.
- The taxonomy ID Kraken 2 used to label the sequence; this is 0 if the sequence is unclassified.
- The length of the sequence in bp. In the case of paired read data, this will be a string containing the lengths of the two sequences in bp, separated by a pipe character, e.g. "98|94".
- A space-delimited list indicating the LCA mapping of each k-mer in the sequence(s). For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
- the first 13 k-mers mapped to taxonomy ID #562
- the next 4 k-mers mapped to taxonomy ID #561
- the next 31 k-mers contained an ambiguous nucleotide
- the next k-mer was not in the database
- the last 3 k-mers mapped to taxonomy ID #562
Kraken 2's standard sample report file format is tab-delimited with one line per taxon. The fields of the output, from left-to-right, are as follows:
- Percentage of fragments covered by the clade rooted at this taxon
- Number of fragments covered by the clade rooted at this taxon
- Number of fragments assigned directly to this taxon
- A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.
- NCBI taxonomic ID number
- Indented scientific name
"
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Would be good to also link your source. (Kraken manual)
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It would be great if you could incorporate all changes until now to your branch. And give a title to each box. Using the titles we can see if we are missing information. |
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This PR is for interactive Galaxy tour for BeerDecoded project |
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