Tapestri Pipeline Getting Started Guide

Welcome to Tapestri Pipeline 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. 

Starting a Run

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

1. Start Run

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

Name the Run

• Add a run name. This is used as the prefix for the output files, any spaces or special characters, such as % & * @ ^ ; “, ' * are replaced by _.
• 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.
  Merge Bulk Runs: This requires at least two Bulk H5s to merge. It supports merging 2 to 6 files. 
• Select the Run Mode Choose one of the modes given below in the dropdown
  Standard - Regular DNA or DNA+Protein runs
  Bulk - DNA runs processed with NGS bulk kit from Mission Bio.
  Genotype Demultiplexing - DNA or DNA+Protein runs multiplexed based on sample genotypes
  Antibody Demultiplexing - DNA+Protein runs multiplexed based on protein expression

  NOTE: Run Mode is the new parameter to process Multiplexed Runs. It is important to set the correct mode as it determines the input for the run. Please read this article for more details.

• Select the Reference Genome (DNA, DNA + Protein)
  Choose either catalog Human (hg19), Human (hg38), Mouse or custom reference file you uploaded in the dropdown menu.
  

  NOTE: Please select the genome Human (hg19) when using the catalog panels - AML, Myeloid, CLL, THP or any of the other Mission Bio uploaded Designer Catalog panels.

• Select Sample Variants File (Genotype Demultiplexing)
  Choose either from Existing Pipeline Generated or User Uploaded Files, or Upload from Local Computer.
• 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: 4 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
  Protein Demultiplexing Panel File: A .csv file, Upload from Local Computer
  
  Number of Files
  DNA: Select or upload one DNA panel file.
  DNA + Protein: Select or upload one DNA and one Protein Panel file.
  DNA + Protein(Antibody Demultiplexing): Select or upload one DNA and one Demultiplexing Protein Panel file.
  
  
• Select Runs To Merge (Merge Samples only)
  Select which runs to merge.
  
  
• Select Bulk H5s To Merge (Merge Bulk Runs only)
  Select which Bulk H5s to merge.
  
  
• Click Next.

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.gz; 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 multiple lanes per run.

Note: To understand how the files are assigned to the lanes, please review the lane assignment rules in the User Guide.

Red and Green Highlighting

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.

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.

• 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.
  
  

  

  For instructions on uploading files, refer to this section.

Click the Start Run button.

Follow these instructions to start the run.