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Hello!
I've seen in the changelog that for DUPs the start position was changed from 0-based to 1-based. What's the case for the rest of the variants, are they 0-based or 1-based?
Best regards,
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Hello! Hope you are well.
I found another small bug in NeoRecoPo.py using a reformatted neoantigens.Indels
Problem stacktrace:
```
INFO: Begin.
Traceback (most recent call last):
File "/…
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Run the example data, I receive this error:
python NeoPredPipe.py -I /mnt/bwa-0.7.17/wes/gatk4/gatk-4.0.6.0/0809_somatic.vcf -H /mnt/bwa-0.7.17/output/arcasHLA/arcasHLA/HLA/HRR572954.genotype.json …
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Hello, I am having an issue using deephlapan.
I used the docker installation on MacOS. When I run the program on a test peptide or a file of several peptides, it stop at the same step.
First, I get…
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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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v %>% foreignness_score(db = "human") %>% print
Removing temporary fasta files.
nmer
1: SIINFEKL
2: ILAKFLHWL
3: GILGFVFTL
Warning message:
In foreignness_score(., db = "human") :
S…
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I reviewed the publication:
https://academic.oup.com/bioinformatics/article/39/11/btad659/7330407
I think that the pipeline used both bam files from RNAseq and DNAseq to call for the long indel. Th…
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Hello
thanks for devolving the neofox alogirhtem. I am trying to build a singularity container and then test the data sets. However, i can't figure out why the test data failed. Can you help to ch…
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Dockerhub Container: mskcc/neoantigenediting:1.0
command: python /usr/bin/align_neoantigens_to_IEDB.py
The workdir needs to have the input in a `data` folder of the structure
data/id_1/id_2/Patie…