User: daniel.magnus.bader

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Posts by daniel.magnus.bader

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Comment: C: Embedded nul \0 in string with Biostrings::readAAStringSet()
... The way I see it, you have to download the bundle with all sequencing files again. If you want to get the "RELEASE.metalink" file that contains the information on the *fasta.gz files from an older version, e.g. "2019_03": ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2019_03 ...
written 5 hours ago by daniel.magnus.bader30
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Comment: C: Embedded nul \0 in string with Biostrings::readAAStringSet()
... Hello Herve, Sorry for sleeping so long. I am just at the next update cycle right now. I wrote my own file parser and do not use `Biostrings` at the moment, but I did not check the sanity of the download again. Uniprot offers this solution for download sanity: https://www.uniprot.org/help/metalin ...
written 1 day ago by daniel.magnus.bader30
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Embedded nul \0 in string with Biostrings::readAAStringSet()
... Dear all, I am creating a local organism-specific version of uniproton on our server. Using the Bioconductor `Biostrings` package I experienced an "embedded nul string" error with the `readAAStringSet()` function, but only on the trembl download, not for the swissprot fasta file. **Q1: Can you ...
biostrings written 4 months ago by daniel.magnus.bader30
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Comment: C: Create protein sequences including variants from a VCF file
... Thanks. Looks like the perfect fit! ...
written 7 months 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 7 months 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 7 months 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 7 months 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 7 months ago by daniel.magnus.bader30

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Student 7 months ago, asked a question with at least 3 up-votes. For Create protein sequences including variants from a VCF file

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