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pogorely / ALICE

Detecting TCR involved in immune responses from single RepSeq datasets
GNU General Public License v3.0
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ALICE with murine data - .rda files #10

Open weshorton opened 5 years ago

weshorton commented 5 years ago

I am attempting to run the ALICE pipeline with murine input data.

From what I've gathered, I'm currently missing two files that are present for human, but lack mouse equivalents:

  1. OLGA_V_J_hum_beta.rda
  2. VDJT.rda

VDJT.rda seems relatively straightforward to produce, but I'm not sure about the other.

I checked out the OLGA documentation and experimented with olga-generate_sequences and olga-compute_pgen, but those outputs do not match up.

Can you please provide details regarding the generation of OLGA_V_J_hum_beta.rda?

jhb1980 commented 3 years ago

Hi @weshorton -- did you manage to get ALICE to work on mouse data? I would also be interested. @pogorely, would you be able to advise?

ArteEfs commented 7 months ago

Hello @weshorton, @jhb1980, @pogorely
Did you have any luck with using ALICE with murine data? It'd be great to know if it's possible. Thanks a lot :)