User: daniel.magnus.bader

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Posts by daniel.magnus.bader

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Comment: C: Create protein sequences including variants from a VCF file
... Thanks. Looks like the perfect fit! ...
written 5 weeks ago by daniel.magnus.bader30
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Answer: A: Create protein sequences including variants from a VCF file
... Thanks to the suggestions from Michael Lawrence and Herve Pages, I guess it should work as follows: 1. Identify all coding SNVs, e.g. via `VariantAnnotation::predictCoding()` 1. Injecting coding SNVs into the genome, e.g. via `BSgenome::injectSNPs()` 1. Concatenate the exons per protein isoform of ...
written 5 weeks ago by daniel.magnus.bader30
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Comment: C: Create protein sequences including variants from a VCF file
... Thanks Herve, However, I think injectSNPs should be sufficient, since I start from genome coordinates in a VCF. Best, Daniel ...
written 5 weeks ago by daniel.magnus.bader30
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Comment: C: Create protein sequences including variants from a VCF file
... Thanks for the reply sheperl. I did not want to start right away with an issue, but now I posted it here: https://github.com/Bioconductor/VariantAnnotation/issues/24 Meanwhile, I will look at `BSgenome::injectSNPs()` which sounds indeed very interesting. Thanks Michael! ...
written 6 weeks ago by daniel.magnus.bader30
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Create protein sequences including variants from a VCF file
... Dear all, I am investigating the proteome of human cancer samples and want to insert their genetic variations into the reference proteome fasta sequences to increase the sensitivity of my peptide/protein quantification. **Can you implement this "proteomeVariantInsertion()" in the VariantAnnotation ...
variantannotation customprodb written 6 weeks ago by daniel.magnus.bader30

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