Comments (2)
Hello, thanks for your interest in nextNEOpi
!
unfortunately we do not support other organisms than human
at the moment. In principle it could be possible to run nextNEOpi
on mouse data, however all the references and databases in the resources
would need to be adapted in first line and there might be other stuff, which of I can not think now, that needs to be changed/extended.
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Hi @saraahwallace I was wondering if you made any progress with that. I have also started investigating the possibility of running nextNEOpi on mouse data. Maybe we could share the ideas? So far, I checked on which MHCs binding affinity tools were trained. I have not attempted identifying resources for genome alignment, variant calling and gene expression. I think identifying which MHCs the mouse has could be a bit tricky computationally but we'll have that information from our mouse model and as I read in the params.config file, it is possible to provide a list. I'm sure there is more stuff to think about as this pipeline uses so many tools :)
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Related Issues (20)
- pVACSeq chmod error HOT 4
- Process `installVEPcache (installVEPcache)` terminated with an error exit status (104) HOT 4
- nextNEO resources bundle installation issues HOT 4
- Failed to run, issues related to pvacseq , etc HOT 5
- Error executing process > 'pVACseq (sample1)' HOT 4
- including SNV/indel calling on RNA-seq data HOT 1
- HLA-HD silently fails if bowtie2 is not installed/loaded HOT 1
- Error executing process "installVEPcache" HOT 7
- How could I improve this pipeline?
- mkfifo: cannot create fifo : Operation not supported HOT 2
- `pVACseq ` terminated with an error exit status (1) HOT 2
- Process `get_vhla (test)` terminated with an error exit status (1) HOT 32
- amino acids sometimes doesn't match the reference or variant HOT 2
- Is .cram input format supported? HOT 1
- 'use_custom_hlas' not defined in the main script or the params file
- mixMHC2pred not triggered when custom HLAs are used HOT 1
- example of custom HLAs
- Process `OptiType_RNA (test_sample)` terminated with an error exit status (1) HOT 13
- pVACtools_generate_protein_seq (test_sample)` terminated with an error exit status (1) HOT 5
- pVACseq (test_sample)` terminated with an error exit status (1) HOT 1
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