hERV and retroelement neoantigens - Githubissues

snakemake-workflows / dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction

MIT License

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hERV and retroelement neoantigens #8

Open dlaehnemann opened 5 years ago

dlaehnemann commented 5 years ago

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.