Tapestri Pipeline Getting Started Guide

  • Updated

Welcome to Tapestri Pipeline v2 for processing single-cell DNA and DNA + Protein sequencing data generated on the Tapestri Platform. 

If you need information about logging into Tapestri Platform, refer to the User Guide. If you used Tapestri Pipeline v1 powered by BlueBee and want to know the differences between v1 and v2, refer to this article.

Starting a Run

There are two ways to start a run – Start Run and Add Files then Start Run.

Add_Files_Start_Run.png

1. Start Run

Click the Start Run button in the top-right corner.

Name the Run

  • Add a run name. Since this is used as the prefix for the output files, it cannot contain spaces or special characters, such as % & * @ ^ ; “, ' *.
  • Add an optional description.
  • Click Next.

Step 01 – Select Pipeline & Other Parameters

  • Select the Pipeline
    Choose DNA, DNA + Protein, or Merge Samples in the dropdown menu.
    DNA: This requires a DNA Panel file and an even number of DNA FASTQ files.
    DNA + Protein: This requires a DNA Panel file and an even number of DNA FASTQ files and a Protein Panel file and an even number of Protein FASTQ files. The number of DNA and Protein FASTQ files must be the same.
    Merge Samples: This requires at least two runs to merge. While the number of runs to merge is currently unlimited, Mission Bio recommends only merging 2 to 5 runs. One .h5 file will be created. When merging DNA and DNA + Protein runs, only the DNA information is retained. Note: Ensure that the merged run name is unique.

  • Select the Reference Genome (DNA, DNA + Protein)
    Choose either Human or Mouse in the dropdown menu.

  • Generate cells.bam file only (DNA only)
    This stops the run after generating the cells.bam file. This sequence alignment file contains only the reads that belong to cells and can be used for genotyping with any tool.

  • Add Panel Files (DNA, DNA + Protein)
    Choose either Select from Existing Files or Upload from Local Computer in the File Source dropdown menu. Click the Add button.

    File Format
    DNA Custom Panel File: A .zip file, Upload from Local Computer
    DNA Designer Catalog Panel File: 5 Preloaded, Select From Existing Files
    Protein Custom Panel File: A .csv file, Upload from Local Computer
    Protein Designer Catalog Panel File: 1 Preloaded, Select From Existing Files

    Number of Files
    DNA: Select or upload one DNA panel file.
    DNA + Protein: Select or upload one DNA and one Protein Panel file.

  • Select Runs To Merge (Merge Samples only)
    Select which runs to merge.

  • Click the Next button.

Step 02 – Select the FASTQ Files (DNA, DNA + Protein)

For DNA runs, select an even number of DNA FASTQ files.
For DNA + Protein runs, select an even number of DNA and Protein FASTQ files. The number of DNA and Protein FASTQ files must be equal.

File Format
Only files with these extensions are allowed: .fastq; .fastq.gz; .fq; and .fq.gz. When importing files from Amazon S3 folders, all the files in the folder and nested folders with the correct extensions will import. All others will be ignored.

To use Amazon S3 or Illumina BaseSpace, first set up the Cloud Connectors. Refer to the User Guide for instructions.

  • In the dropdown, choose Select from Existing Files, Upload from Local Computer, Import from Amazon S3, or Import from Illumina BaseSpace in the Select FASTQ Files dropdown menu.
  • Click the Add button.

    1. Select from Existing Files
    Click the checkbox to the left of all the files you want to include.
    Click Done.

    2. Upload from Local Computer

    DNA
    Drag and drop the DNA FASTQ files into the upload area or click Choose Files.

    DNA + Protein

    Drag and drop the DNA FASTQ files into the upload area or click Choose Files.
    Choose Protein FASTQ from the dropdown menu, and drag and drop the Protein FASTQ files into the upload area or click Choose Files.

    Click Upload.

    3. Amazon S3
    To add multiple files or folders, separate the names with either a "," or ";".

    DNA
    Add the Amazon S3 URI for the DNA FASTQ files or the folder containing the FASTQ files.

    DNA + Protein 
    Add the Amazon S3 URI for the DNA FASTQ files or the folder containing the FASTQ files.
    Click +Add FASTQ files for another analyte.
    Select Protein FASTQ.
    Add the Amazon S3 URI for the Protein FASTQ files or the folder containing the FASTQ files.

    Click Import.

    4. Illumina BaseSpace

    To add multiple biosamples, separate the names with either a "," or ";".

    DNA
    Add the Biosample Name for the DNA FASTQ files – Project ID: Biosample name.

    DNA + Protein 
    Add the Biosample Name for the DNA FASTQ files – Project ID: Biosample name.
    Click +Add FASTQ files for another analyte.
    Select Protein FASTQ.
    Add the Biosample Name for the Protein FASTQ files – Project ID: Biosample name.

    Click Import.

  • Click the Next button.

Step 03 – Lane Assignment (DNA, DNA + Protein)

Tapestri Pipeline auto assigns FASTQ files to the lanes. If you prefer to assign the files yourself, click the Reset button in the left panel. The files will then go into the right panel where you can drag and drop them into the correct lane location. Each lane should have 2 files, one R1 and one R2. You can have up to 4 lanes per run.

Note: Depending on the chemistry used to generate the FASTQ files, the sequencing library may have 1 or more pairs of FASTQ files in a run. If this is the case, there will a dropdown with the number of pairs instead of the static 1 in the image above. Please review the lane assignment rules in the User Guide.

Red and Green Highlighting

Red_Green_Highlights.png

The green color indicates that the files follow the lane assignment rules we expect. For example, L001 indicates Lane 1. R1 denotes R1.

If the color is red, the file does not match our lane assignment rules. You can submit the run, but double-check to see that the files are in the correct location. Please review the lane assignment rules in the User Guide.

  • Verify the file assignments for the DNA FASTQ files and Protein FASTQ files, when applicable.
  • Click the Next button.

Step 04 – Preview

This is the final step before submitting the run. Confirm all the information. To edit any of the information, click the Edit icon next to the Steps or click the Step in the left Panel.

Preview_Edit.png

After confirming all the information, click Submit Run.

Run Successfully Submitted

Once the run is submitted, you have the option to Submit Another Run or Go To Runs Page.

Submit Another Run

This option clones the current run. Name the run and adjust any of the parameters.

Go To Runs Page

This option returns you to the main Runs page.

2. Add Files then Start Run

This option allows you to upload files before starting a run.

Add_Files_Start_Run.png

  • Click Add Files.
    There are three ways to upload FASTQ files – Upload from Local Computer, Import from Amazon S3, and Import from Illumina BaseSpace. Panel files can only be uploaded from a local computer.

    Add_Files.png

    For instructions on uploading files, refer to this section.

Click the Start Run button.

Follow these instructions to start the run.

Share this article:

Was this article helpful?

2 out of 2 found this helpful

Have more questions? Submit a request