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Hello NeoPredPipe developers:
I am using the latest version of NeoPredPipe. I cloned the repo two days ago and saw that there are some updates about dectecting type-II HLA neoantigens. But I can't …
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Hi developers, first of all thank you for putting together this resource.
I am trying to run the NeoRecoPo.py and I am getting some errors. Before detailing those errors, I just want to make sure t…
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Hello,
I run NeoPredPipe using the data in the Example directory with the flowing command:
python main_netMHCpan_pipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun…
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Run the test data as the flowing:
**step1**
python main_netMHCpan_pipe.py --preponly -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10
INFO: Annovar r…
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Hi:
I developed a perl script [NeoPredPipe.install.pl](https://github.com/wangshun1121/NeoPredPipe/blob/master/NeoPredPipe.install.pl) to deploy latest NeoPredPipe, using following command:
```…
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Hello
I had run your software on my data wrongly put `c 1 2 parameter ` instead of `c 1` while my vcf files are single region so I have a results like
![Untitled](https://user-images.githubuser…
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Hello
I have some .vcf files but I don't have access to raw sequencing data or any patient specific HLA typing
I want to predict neoantigen load for my patients (of proving mutation burden)
I…
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Hello
I have a set of vcf files (SNVs) from patients who have responded to chemotherapy versus a set of patients who have not responded.
I want to quantify the neoantigen load in the tumors ,can…
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Hi,all
I have tested about 30 samples for MHC-II type. They all worked well, but the result seemed quite different with that of MHC-I. The MHC_II neoantigens.Indels.txt was as following:
xq009…
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Hello.
As far as I can understand - the main reason for using your own [netmhccons_1_1_python_interface.py](netmhccons_1_1_python_interface.py) are these lines:
```
#process_status_code = p.wai…