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snakemake-workflows / dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction

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hERV and retroelement neoantigens

dlaehnemann opened this issue · comments

commented

Neoantigens generated by tumor-specific expression of retroelements (LINEs, SINEs, hERV, etc.). They require a differential expression analysis between tumour and normal samples, to ensure that the element is not expressed in the normal cells.

Available tools:

  • hervQuant

Alternative idea:

  • Create reference sequence database of such elements and do kallisto + sleuth differential expression analysis, then turn tumour-only elements into potential peptides.