Can my IGH seq data be analyzed by this pipeline?

[fabio li]

Hello, I just started my first IGH sequence analysis project recently. I want to use this pipeline to define clones and do some lineage analysis, but my data is from bulk VDJ seq, I didn’t find literature using Change-O to analyze the such data, many literatures using similar sequencing methods and Change-O have added UMI in the sequencing process. Although I don't think UMI should interfere with my analysis process, I'm still not sure. Can you help me out with this please?

[ssnn]

Hi Fabio,

Yes, you can use Immcantation. For raw data processing, you need to use pRESTO. A good place to start to learn how to use it, is looking at the examples in https://presto.readthedocs.io/en/stable/ To understand the different steps in downstream analysis, check the introductory tutorial here https://immcantation.readthedocs.io/en/latest/tutorials/tutorials.html. If you have questions, you can email the Immcantation Group ([e-mail]).

[fabio li]

Thank you for your help :)

[fabio li]

Just realized I shouldn’t create such a issue in “bug or feature request” zone : ( , new to github/bitbucket as well. I just changed status to closed hoping this won’t influence others' normal browse, or you can just delect this issue if it’s possible. sorry for the inconvenience.