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Use Case 3-2

Use Case 3-2's aim

In this Use Case, Metavisitor is used to search for the presence of viruses and identify them in RNA sequencing data of serums of children suffering from fevers of unknown origins. To compare Metavisitor's results to Yozwiak et al.

Input data for Use Case 3-2

As for the previous Use Cases 1, 2 and 3-1, the first step is to collect all input data in an history that we will name Input data for Use Case 3-2.

  • Create a new history
  • Rename this history Input data for Use Case 3-2
  • Using the tool Extract reads in FASTQ/A format from NCBI SRA, we are going to upload 43 paired end datasets. Indeed, these 43 datasets correspond to 86 fastq paired-ended sequence files. In addition, some datasets derive from the same patient; in those cases we will merge those datasets using the tool Concatenate multiple datasets tail-to-head and delete and purge the original datasets.

  • Open the "Upload datasets" menu. Click on the Paste/Fetch data button, name the file "Use-Case_3-2_SRR_information" and copy-paste the following text:

    SRR id Patient id
    SRR453487 patient 566
    SRR453437 patient 438
    SRR453443 patient 401
    SRR453458 patient 401
    SRR453430 patient 382
    SRR453491 patient 377
    SRR453499 patient 375
    SRR453484 patient 350
    SRR453464 patient 349
    SRR453506 patient 345
    SRR453417 patient 344
    SRR453490 patient 335
    SRR453478 patient 331
    SRR453465 patient 330
    SRR453480 patient 330
    SRR453489 patient 329
    SRR453505 patient 329
    SRR453498 patient 322
    SRR453446 patient 321
    SRR453427 patient 315
    SRR453440 patient 315
    SRR453438 patient 282
    SRR453450 patient 275
    SRR453460 patient 274
    SRR453485 patient 270
    SRR453448 patient 266
    SRR453424 patient 263
    SRR453457 patient 263
    SRR453510 patient 193
    SRR453456 patient 187
    SRR453425 patient 186
    SRR453469 patient 186
    SRR453481 patient 183
    SRR453531 patient 180
    SRR453474 patient 179
    SRR453509 patient 171
    SRR453451 patient 168
    SRR453495 patient 161
    SRR453504 patient 161
    SRR453500 patient 159
    SRR453493 patient 156
    SRR453444 patient 131
    SRR453426 patient 78

  • Click the Start button.

  • Select the Cut columns from a table tool and set the "Cut columns" parameter to "c1" and select "Use-Case_3-2_SRR_information" as input file in the "From" list. Execute the tool and rename the new dataset collection "Use_Case_3-2_accessions".
  • Select the tool Download and Extract Reads in FASTA/Q format from NCBI SRAand select "List of SRA accession, one per line" in "select input type" and "Use_Case_3-2_accessions" in "sra accession list". Execute the tool. The data downloading step might take 40 minutes to 1h. Delete "Single-end data (fastq-dump)".
  • Select the Concatenate multiple datasets tail-to-head tool and set "Paired collection" in "What type of data do you wish to concatenate?" and "Pair-end data (fastq-dump)" as "Input paired collection to concatenate". In "What type of concatenation do you wish to perform?" select "Concatenate pairs of datasets (outputs an unpaired collection of datasets)". Execute the tool.
  • Select Tag elements from file tool and set "Concatenation by pairs" as "Input Collection" and "Use-Case_3-2_SRR_information" as "Tag collection elements according to this file". Execute the tool.
  • Select Apply Rule to Collection tool and set "data 1, data 144, and others (Tagged)" as "Input Collection" and click the "Edit" button.
    • Click the "Column" button and select "Add Column from Metadata" from the list.
    • Select "Tags" from the "For" list and click the "Apply" button.
    • Click the "Rules" button and select "Add / Modify Column Definitions".
    • Click "Add Definitions" button and select "List identifier(s)" from the list.
    • Select "B" from the "Select a column" list.
    • Click "... Assign Another Column" and select "A" from the "Select column" list. Click the "Apply" button and the "Save" button. Execute the tool.
  • Select the Conatenate multiple datasets tail-to-head tool ans set "Nested collection" in "What type of data do you wish to concatenate?" and select the "... (re-organized)" dataset collection in "Input nested collection". Click the "Execute" button.
  • Rename the output collection as "Tractable Patient Datasets".
  • Copy the vir2 nucleotide BLAST database from the References history to the current history Input data for Use Case 3-2.

History for Use Case 3-2

  1. Stay in the history Input data for Use Case 3-2
  2. pick the workflow Metavisitor: Workflow for Use Case 3-2 in the workflows menu, and select the run option.
  3. For Step 1 (Fever Patient Sequences collection), select Tractable Patient Datasets (this should be already selected).
  4. For Step 2, select the nucleotide vir2 blast database (this should also be already selected)
  5. As usual, check the box Send results to a new history, edit the name of the new history to History for Use Case 3-2, and Execute the workflow ! Note, that for complex workflows with dataset collections in input, the actual warning that the workflow is started make take time to show up; you can even have a "504 Gateway Time-out" warning. This is not a serious issue: just go in your User -> Saved history menu, you will see you History for Use Case 3-2 running and you will be able to access it.

As a last note, the workflow for Use Case 3-2 may take a long time. Be patient.