Running ATX epigenomic preprocessing | Scribe

    Running ATX epigenomic preprocessing

    • Jen Garbarino |
    • 14 steps |
    • 2 minutes
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    This workflow takes fastq files and aligns them using chromap to the genome as well as outputting QC metrics for the run and other files using cisTopic.
    1
    Click on the workflows button in LatchBio to go to the workflows tab
    2
    Click on the ATX epigenomic preprocessing
    3
    Input the run id for this sample
    4
    Next we will enter read 1 from the paired end sequencing
    5
    Click "Select File" and then navigate to where read 1 is located. Click select once file is found
    Click "Select File" and then navigate to where read 1 is located. Click select once file is found
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    Make sure your fastqs are compressed to use the workflow (fastq.gz)
    6
    Input read 2 of the sample in the same manner
    7
    Click "Select File" and then navigate to where read 2 is located. Click select once file is found
    Click "Select File" and then navigate to where read 2 is located. Click select once file is found
    8
    Select the genome for chromap to align
    9
    Click "Select Folder" and go to "Chromap_references". Click the genome you wish to align to and click "Select". If you need additional references contact AtlasXomics
    Click "Select Folder" and go to "Chromap_references". Click the genome you wish to align to and click "Select". If you need additional references contact AtlasXomics
    10
    Choose the barcode file corresponding to the chip version run for your sample
    11
    If running a spatial assay click here to perform peak calling in pseudo bulk for this sample. This is not recommend for runs with over 200 channels or very deeply sequenced runs.
    12
    If sequencing a bulk optimization assay, click the bulk button
    13
    Select the toggle for bulk if using our standard bulk optimization kit. If you are doing a no-ligation primer bulk select the other toggle. These will ensure the format of the reads is consistent for the alignment by assigning random barcodes to each fragment.
    14
    Click "Launch Workflow" to begin processing. Outputs will be available in the chromap_outputs folder