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Hi,
After solving patch error (issue#14) by installing patch in our computation node, the pipeline run into a new error
```
Caused by:
Process `mixcr (Patient353_T1star : tumor_DNA)` termina…
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* pvactools version: 1.5.2
* Python version: 3.7.3
* Operating System: red hat 6
I ran pvacseq with NetMHCpan and NetMHCpanII. The combined filtered output (295 lines) has is less than the lines …
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Hi
I am wondering what is the best way to visualize the clones in a tree in order to accurately assess of the evolution or monoclonal or polyclonal.
I tried to check the stories Rdata and checked…
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We have followed the procedure in: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf for evaluating potential neoantigens using no-enzyme.
PepQuery2 does not have option: -tag
Does …
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Our current reliance on INTEGRATE (for fusion detection) and INTEGRATE-NEO for annotation of the fusion junction peptide is problematic.
It would be desirable if we could support fusion calls from …
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Although I use 3-way in-silico translation, a lot of time, proteins prefer to use one ORF, so we want to annotate each obtained T antigen to prioritize certain neoantigens for experimental validation.
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Hi
I am trying to run the pipeline locally. However, the pipeline run very slow in get_vhla step. This step already took more than 5 days. I wondered if this is normal situation or the pipeline fal…
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We need to create clean versions of the following tables for the upcoming data freeze:
**Quality tables**
- [x] analysis.gene_coverage
- [x] analysis.blocklist
- [x] analysis.coverage
- [x] ana…
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Hi everyone!
Testing the installation resulted in the following error for me:
```
# neofox --candidate-file test_data.tsv --patient-data test_patients.tsv --output-folder output --with-table --w…
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Hi! I tried to use nextNEOpi and received the following error:
Unknown method `div` on ConfigObject type
My code:
nextflow run nextNEOpi.nf --readsTumor /work/Projects/Neoantigens_nextNEOpi/tes…