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Error received:
```
Traceback (most recent call last):
File "/Users/Ryan/anaconda2/bin/topiary", line 64, in
main()
File "/Users/Ryan/anaconda2/bin/topiary", line 46, in main
epitopes = …
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Hi,
Is it possible to change the filter for peptide length for predictions ?
Although the default (8 to 12 residues) can work well for some allotypes, others may include shorter or larger peptides…
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@leonjessen I tried this variation of the model that treats the peptides as sequences (this is under the assumption that the order of the peptides actually matters, this may or may not be the case, yo…
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This issue is about mass spectrometry data (MS), we have not made a decision about whether to include the data or not. We want our affinity predictor to have no bias towards peptides that are processe…
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can you give some advice, thanks a lot
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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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Hi,
I am attempting to use antigen garnish to predict neoantigens from fusion proteins predicted by arriba/starfusion/fusioncatcher.
I took the predicted peptides from those programs (quite long, mi…
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Hi,
I have run the NeoPredPipe.py as:
`python NeoPredPipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10`
INFO: Annovar reference files of build h…
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I copied test data from example_data folder provided by the neoflow.
the input_vcf_list.txt file looks like:
```
experiment sample file file_type
crc_test sample1 /neoantigen2/inpu…
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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…