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I have a few questions regarding the `garnish_antigens` filtering.
The documentation says, that the tool returns a data frame with ranked neoepitopes.
I was wondering if you could elaborate how exa…
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Hi,
I came across your pipeline not long ago and found it would be great for my research so I am really keen to make sure I can get it running.
I set the pipeline up and did not input the HLA-HD…
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Running the following command results in failure:
```
pvacseq run \
--iedb-install-directory /opt/iedb \
-t 10 \
-p test_vep_phased.vcf.gz \
-e1 8,9,10,11 \
-e2 15,16,17,1…
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Hello Andrew,
I have a couple of questions regarding the antigen garnish output file:
1. There is a column called pep_type with three different types (wt, mutnfs and mut_other), does this mean tha…
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Hi, I am testing pVACseq workflows and first of all thanks for your great work!
I have successfully generated all_epitopes.tsv and the filtered.tsv using mhcflurry. But when using NetMHC, I only got …
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So that we can run @iskandr's pipeline on it and get a short-list of "neoepitopes" that we can work our way through.
Submitted MC38B cell pellets (as well as PBMCs from B6 mouse as our normal) to G…
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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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Hi,
After I installed the tool, test it ,but some errors happened:
```
epitopepredict -n -t
wrote config file default.conf
Traceback (most recent call last):
File "/public/slst/home/wutao2…
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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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Error occurs after multiple warnings with message "Stop codon not detected prior to end of transcript {transcript_name}; this transcript may undergo degradation".
**Neoepiscope version: 0.4.1**
…