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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Using the pipeline on cell line data #81

Closed GMFranceschini closed 1 month ago

GMFranceschini commented 1 month ago

Dear developers, Could you advise me on running the pipeline on cancer cell line data? In that case, we don't have the normal DNA, could we use a random individual or a panel of normals? I know it's not an ideal setting, but I would still like to try to get neoantigens. Thank you in advance

riederd commented 1 month ago

Hi, thanks for your interest in nextNEOpi. Technically you may use DNA from any normal and in addition a panel of normals and the pipeline would run, however this will most likely give you random results, I'd not advise to do so unless it is just for playing/testing.