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I'm having a trouble running protect, and figuring out what exactly is failing, as the output is 4655 lines long.. I'm most probably just missing some parameters, but I'm not sure which ones exactly. …
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child of #3
arkal updated
6 years ago
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I've run all the preliminary steps without problem (HapCut2, prep) but the final 'call' step has been running for over a week now, using 1 cpu, and stable at a couple GB of RAM. It also output (not su…
jfass updated
4 years ago
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Hi Charles and Peter,
Is it possible to specify the length of the epitopes in the output from Neo? By default it is 31 for missense variants (15 aa upstream + 1 novel + 15 aa downstream). I'd like…
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This [paper ](https://doi.org/10.1084/jem.20190179)defined anchoring residues for 6 of the MHC-I mice alleles, for 8, 9, 10 and 11-mer peptides, and found increased discrimination of immunogenic neoep…
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Hi, I try to generate noepeptide using this pipeline recently but encounter some difficulties.
firstly, I successfully run this pipeline with both somatic and germline variant which called by vars…
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### Description of the bug
The process `GENERATE_PROTEINS_FROM_VCF` and the underlying script `variants2fasta.py` need to get a complete overhaul. A few issues I ran into:
- At least [variant of…
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Hi,
I tried to use the following script to get the mismatching output:
```
from pepmatch import Preprocessor, Matcher
Preprocessor('proteomes/human.fasta').pickle_proteome(k = 3)
Matcher( …
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Hi,
I noticed that there is an issue with the latest release of the package. In the netMHC.py code line 45 should be changed from:
`if line.startswith(" 1 HLA"):`
to
`if re.match(r'^\s+1 …
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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…