User: daniel.magnus.bader

Reputation:
30
Status:
New User
Location:
Last seen:
2 months ago
Joined:
6 months ago
Email:
d******************@gmail.com

Posts by daniel.magnus.bader

<prev • 6 results • page 1 of 1 • next >
0
votes
0
answers
77
views
0
answers
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 9 weeks ago by daniel.magnus.bader30
0
votes
1
answer
196
views
1
answers
Comment: C: Create protein sequences including variants from a VCF file
... Thanks. Looks like the perfect fit! ...
written 5 months ago by daniel.magnus.bader30
0
votes
1
answer
196
views
1
answers
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 months ago by daniel.magnus.bader30
0
votes
1
answer
196
views
1
answers
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 months ago by daniel.magnus.bader30
0
votes
1
answer
196
views
1
answers
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 5 months ago by daniel.magnus.bader30
3
votes
1
answer
196
views
1
answer
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 5 months ago by daniel.magnus.bader30

Latest awards to daniel.magnus.bader

Student 6 months ago, asked a question with at least 3 up-votes. For Create protein sequences including variants from a VCF file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 286 users visited in the last hour