Running the Create ArchRProject workflow | Scribe

    Running the Create ArchRProject workflow

    • Jen Garbarino |
    • 22 steps |
    • 2 minutes
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    This workflow is intended to be used after clustering parameters were selected in optimize archR. this workflow only uses one set of clustering parameters and does peak calling as well as motif enrichment. It creates many more outputs and figures for downstream analysis.
    1
    Click on the workflows button in LatchBio to go to the workflows tab
    2
    Click on the create ArchRProject workflow
    3
    To add your sample click add a row
    4
    Enter the Run_id here
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    Run_id should not have any spaces and cannot start with or be a single number. This needs to be a unique identifier for every sample in the project
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    If you have an additional name for the sample, input it here
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    Next associate the fragments file for this Run_id
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    To find the fragment file in LatchBio, click select file. Navigate to the fragment files and click "Select".
    To find the fragment file in LatchBio, click select file. Navigate to the fragment files and click "Select".
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    Service run fragment files will be located in the Raw_Data folder.
    8
    Enter Condition if applicable to samples. You can leave this blank.
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    No spaces allowed within condition. If you have two conditions you can separate with a dash (dash cannot be used within condition). example: "post_treatment-non_resonder" will give you two conditions: post_treatment and non-responder. "post treatment-non-responder" will lead to errors.
    9
    Next we will input the location of the spatial directory. This folder is generated by AtlasXbrowser and is needed to connect the data to the imaging done of the sample.
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    Click "Select Folder"\ Navigate to the location of the spatial folders. Select the folder called spatial within the Run_ID labelled folder
    Click "Select Folder"\ Navigate to the location of the spatial folders. Select the folder called spatial within the Run_ID labelled folder
    11
    We also will associate the position file for the sample here. This file determines where on the image the data is located and which datapoints contain tissue and should be included in the analysis.
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    Click "tissue_positions_list.csv" to specify the tissue position list within the folder and click "Select".
    Click "tissue_positions_list.csv" to specify the tissue position list within the folder and click "Select".
    13
    For additional samples click add a row and follow the above steps to add their information
    14
    Set genome for experiment (mm10-mouse, hg38-human) contact AtlasXomics if you need an additional reference genomes added
    15
    Enter a project name to call this workflow execution. Project name cannot contain spaces and will be the name of the output folder for this execution.
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    The next few parameters are able be optimized in our optimize archR workflow to prevent multiple runnings of create archRProject