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I am trying to apply fastq files of RNA-seq (paired-end) to NeoFuse to identify neoantigens.
My fastq files may contain low quality bases and adapter sequences. Should I prepare fastq files that excl…
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thnanks a lot for the kind help
latest docker pvacseq
**Describe the bug**
I ran pvacseq, but it does not throw any error , but the pocess in ps aux become Z
**To Reproduce**
docker run -…
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I've been running tests of the latest version on R 4.1.0 using the inbuilt examples.
library(magrittr)
library(data.table)
library(antigen.garnish)
# load an example VCF
dir %
file…
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Hello!
What is the run time estimation for the correction of the long reads? I used the default command for running Ratatosk `Ratatosk correct -v -c 90 -s short_reads.fastq -l long_reads.fastq -o o…
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Hello, I was wondering if there was an argument option to output the wildtype epitope that the mutant epitope arose from? I can't back calculate the wild type epitope even though there is an output fi…
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Hi,
Sorry to bother again.
I used following code to perform neoantigen recognition potential predictions:
```
NeoRecoPo.py -d --neopred_in=test.txt --neoreco_out=./ --fastas=./test
```
But some …
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Hi,
I use the following code to predict neoantigen :
```
NeoPredPipe.py -I ./test/ -H ./TCGA_HLA_typing.txt -o ./test_results -n TCGA-02-0047-01A -c 0 -E 8 9 10 -x exp/
```
The `test_result` di…
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Hi, Thanks for the great software!
* pvactools version: docker images pVACtools:2.02
* Operating System: ubuntu 20.04
**Describe the bug**
When I ran pVACseq with the PHASED_PROXIMAL_VARIANTS_…
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For example, from this paper: [Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing](https://www.ncbi.nlm.nih.gov/pubmed/25428506):
Gene | Peptide | MHC allel…
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Dear developers,
Thank you very much for the useful tool. I built Python2.7 with conda, and configure the 'usr_path.ini' file for my environment.
Then I run `python NeoPredPipe.py -I ./Example/i…