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In this page you will find our recommendations on how to processes each data type available in Qiita and the minimum processing requirements to make your data public.
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For convenience, there is a "Add Default Workflow" button on each preparation, that will allow you to add all this steps to
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your raw data; however, all data is different and some of these steps will not work with it so we recommend checking that at least
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the initial steps work for your data. An example of this, for target gene we assume you are uploading raw multiplexed EMP data with
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reversed barcodes in your mapping file and index sequence file (EMP default). If that specific step doesn't apply to your data, you
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can add and run whatever processing steps makes the most sense to your data and then add the rest of the steps by using that button.
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For convenience, there is an "Add Default Workflow" button for each preparation that will add the recommended workflow steps for your raw data which then you can process.
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It is important to note however that some steps it this default workflow will not work with all raw data; for example, for target gene the workflow is based on the
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default Earth Microbiome Project protocol and so assumes the uploaded data are multiplexed sequences with the reversed barcodes in your mapping file and index sequence
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file (<ahref="https://earthmicrobiome.org/protocols-and-standards/" target="_blank">see here</a> for more details). Thus, if the protocol does not apply to your data
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you can still use the Default Workflow, however, you should first manually process your data using the appropriate steps until you have a defined step; in our example,
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demultiplexed your reads. After demultiplexing the Default Workflow is safe to use with any protocol.
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By the way, if you have already performed one of the processes in this pipeline, the button "Add Default Workflow" will not re-run that step but instead will
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run any other steps that havehas not been completed.
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If you have already manually performed one of the processing steps in the Defaul Workflow pipeline, the "Add Default Workflow" button will not re-select those steps but
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instead will only select any remaining steps that have not been completed. You can also add additional workflows on top of the recommended Default Workflow at any time.
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Note that this is not a full inclusive list of data types accepted by Qiita but those that have a <u>defined</u> workflow.
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Note that this is not a full inclusive list of data types accepted by Qiita but only those that have a defined workflow.
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<h5>Hover on the spheres to get more information</h5>
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