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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Cross-species compatibility #24

Open saraahwallace opened 1 year ago

saraahwallace commented 1 year ago

Hello, I am attempting to use nextNEOpi for my honours project analyzing some mouse data. Is it possible to use nextNEOpi on data from other species. If yes, what sort of parameters need to be changed? At this stage the error seems to be coming from GATK not being compatible with the mouse data. Any help appreciated, Sarah.

riederd commented 1 year ago

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.

mantczakaus commented 1 year ago

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 :)