Output file discriptions

[rezakj]

Hi,

I have 2 questions:

1- Is there a better documantion of the output files?

2- In the "neoantigens/sample1/Class_II/" diretory the following files are missing: sample1_MHC_Class_I_all_epitopes_ccf_ref_match.tsv, sample1_MHC_Class_I_filtered_ccf_ref_match.tsv. Do you know why is that?

[riederd]

Hi, thanks for your interest in nextNEOpi

@1 You can find more information in the supplemental material of our publication https://doi.org/10.1093/bioinformatics/btab759

@2 In the Class_II directory you should not find MHC_Class_I related/named files, because it is only for MHC_Class_II results.

[rezakj]

Oh sorry, I copy pasted the file name from class I but I meant this file (classII):

sample1_MHC_Class_II_all_epitopes_ccf_ref_match.tsv

There is only a fusion folder in it.

[riederd]

Can you attach the .nextflow.log file, so that I can check?

[rezakj]

Attached.

slurm-20852100.out.log

[riederd]

It seems that you did not specify the path to your local HLA-HD installation.

Your slurm-20852100.out.log, which bwt is not the .nextflow.log, shows: WARN: WARNING: HLAHD not available - can not predict Class II neoepitopes

Here is the relevant section from the README.md:

Optional but recommended: Due to license restrictions you may also need to download and install HLA-HD by your own, and set the installation path in conf/params.config. If HLA-HD is not available Class II neoepitopes will NOT be predicted

Unfortunately we are not allowed to bundle and distribute HLA-HD, therefore nextNEOpi users need to install it manually on their system if they want to also predict Class II neoepitopes.

HTH, closing this ticket for now

[rezakj]

Thank you. Reza