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> Traceback (most recent call last):
> File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRecoPo.py", line 135, in
> main()
> File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRe…
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Hi,
I had recently been able to run the nextNEOpi pipeline through (after some minor modification). When looking at the results section I noticed that the `./results/neoantigens/[sample]/Class_II`…
dmgie updated
2 months ago
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Ideally we should keep forks of pVACtools and conpair in the umccr GitHub org.
- We currently use this fork of pVACtools inside the [neoantigens conda env](https://github.com/umccr/umccrise/blob/be…
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Thank you for sharing your fasinating work. When I use it, I find all my TCR-pMHC get a very high rank which in your paper represent high possibility for binding. But, in our perspective it can be pos…
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Hello!
I am testing the pipeline with netMHCpan version 4.1 and all is working as expected.
To convert the neoantigens output to the format required by `NeoRecoPo.py ` should be sufficient to …
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hi, your tool is wonderful and your tutorials are very detailed. However, I encountered this error when running the T antigen workflow.
In [14]: snaf.JunctionCountMatrixQuery.generate_results(path=…
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HI:
I want to use NeoRecoPo.py to get Neoantigen Recognition Potential. I used the data you provided to run the project.
**step1:**
`/usr/bin/python NeoPredPipe.py -I ./Example/input_vcfs -H ./Exa…
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AC:
- Add table to database called neoantigens with columns
- patient_id (foreign_key)
- feature_id (foreign_key)
- gene_id (foreign_key)
- tpm
- Add query to api that
- re…
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Hi, I have been trying to run antigen garnish for a while with your testdata and now it seems to run fine with parallel and netMHC. The issue is that in the folder as e.g. ag_f236b988a09e438ea2 it doe…
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Hello, thank you for providing this tool. I have some confusion regarding the interpretation of the output results. How can I understand the affinity and immunogenicity from the BigMHC_EL and BigMHC_I…