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elkebir-group / TRIBAL

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Preprocessing and input files #1

Open Jiawei-Xing opened 2 months ago

Jiawei-Xing commented 2 months ago

Hello, I'm very interested in using TRIBAL on a 10x scRNA-seq dataset, but I'm a bit confused of how to prepare for the input files and get started. Could you please share some details of the methods you used in the manuscript:

  1. Generating ai and bi for each cell i using Cell Ranger
  2. Assigning clonotypes using Dandelion
  3. Identifying clonotype MSAs using Dowser
lweber21 commented 2 months ago

Glad to hear you are interested in using TRIBAL. We are currently working to put together some additional documentation and helper scripts for preparing the TRIBAL input data and hopefully we will have that out in the next couple of weeks. In the meantime, I can point you to the online tutorials for the existing tools where there is a wealth of documentation:

Our internal TRIBAL preprocess tool will find the MSAs for each clonotype and the Parsimony Forest and we recommend using that so there is no need to run dowser.

xinyu-g commented 4 days ago

Hi, I wanted to share that we recently added a repo to preprocess single-cell BCR/TCR data from the 10x Genomics 5’ solution for TRIBAL analysis: https://github.com/elkebir-group/TRIBAL_Dandelion_Preprocess. Let me know if this is helpful for your datasets or if there is any issue you run into using it. @Jiawei-Xing