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Bcbio-nextgen tutorial » History » Version 5

Bryan Cosca, 03/16/2015 07:01 PM

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h1. Running bcbio-nextgen using Arvados
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WIP
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h2. Uploading data through the web and using it on Arvados
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# In your home project, click on the blue *+ Add data* button in the top right.
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# Click *Upload files from my computer*
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# Click *Choose Files* and choose the 2 paired end fastq files you would like to run bcbio-nextgen on.
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# Once you're ready, click *> Start*
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# Feel free to rename your Collection so you can remember it later. Click on the pencil icon in the top left corner next to *New collection*
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# Once that is uploaded, navigate back to the dashboard and click on *Run a pipeline...* and choose bcbio-nextgen pipeline.
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# You can change the input by clicking on the *[Choose]* button next to the *R1 parameter* and *R2 parameter*.
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# Input your left fastq file as R1 and your right fastq file as R2.
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# For each fastq file, click on the dropdown menu, click on your newly-created project, and choose your desired input collection. 
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# Click *Run* to run bc-bio on your data!
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h2. Uploading data through your shell and using it on Arvados
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WIP
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h3. FAQ
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WIP