Frequently Asked Questions

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Project Management

Can I copy a file from one project to another?

Answer: No. We will support this feature in a future release. For now, you need to upload your file into the other project.

VDJPipe Workflows

Why do I not get any output files with Barcode Demultiplexing from VDJPipe?

Answer: Check the summary.txt file generated from the Job to see if the Match step is removing all of the reads. This can happen for a number of reasons:

  • The search window is specified is too small.
  • Make sure you are specifying the correct 5' or 3' end of the sequence read to search for the barcode.
  • Is the correct barcode file provided? You may want to manually verify that you can find the barcode sequence with a handful of your sequence reads.
  • 3' barcodes currently (VDJServer Ver. 1) need to be provided in the forward orientation. 3' barcodes are often given in the reverse orientation.
  • Incorrect orientation was specified for your reads.

Hint: Extract a subset of your reads, e.g. 100 reads, from your dataset and use those for testing. Those jobs will run quicker.

How do I handle multiple barcodes?

Answer: You can run the Barcode Demultiplexing workflow multiple times to handle multiple barcodes. A future release of VDJServer will allow the user to specify any custom barcoding scheme. For now, we have provided instructions for many of the common barcoding scheme found in the literature.

IgBLAST Workflow

What is the cutoff for alignment results? Is it based upon percent identity?

Answer: VDJServer use the default parameters in IgBlast for alignment of the V, D and J genes, which is a cutoff E-value of 1.0. This varies from sequence to sequence for actual identity percentage, but it is a fairly loose constraint. By default, VDJServer returns the top scoring alignment. In the resultant summary TSV file, the column Sequence similarity provides the actual percentage identity. The columns Alternate V gene, Alternate J gene, and Alternate D gene will give you the other genes that were returned from the alignment.

Job Results and Analyses