User: asd

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asd10
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Posts by asd

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Mutect2 error - Cannot merge sequence dictionaries
... I downloaded two BAM files from the TCGA Legacy repository, [a normal BAM][1] and [a tumor BAM][2] for the same patient. I tried to process the files with Mutect2, but I got an error: > ##### ERROR AN INPUT FILE ERROR has occurred (version 3.7-0-gcfedb67): > ##### ERROR MESSAGE: Cannot merge ...
wxs tcga bam mutect2 written 3.4 years ago by asd10
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Comment: C: Get protein domain information from gene name in R
... For TP53 the bioMart unique tsv contains 17 row but the Pfam website just 13. BioMart has domain from 1 to 156, Pfam has 1 to 23. Why is this difference? ...
written 3.6 years ago by asd10
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Comment: C: Get protein domain information from gene name in R
... Thank you, bioMart returns the required results, but it contains too much row and not just those, which annotated as 'Pfam' and 'low_complexity' on [Pfam website][1]. How can I annotate it with this source and domain column? [1]: http://pfam.xfam.org/protein/p53_HUMAN ...
written 3.6 years ago by asd10
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Get protein domain information from gene name in R
... I would like to get the protein domain name, start and end of a gene by its name in R. A Web API is also acceptable. My goal is to plot DNA mutations on protein domain level, like the cBioPortal MutationMapper, but I would like to do it programmatically in R. I know that this information available ...
R protein package written 3.6 years ago by asd10 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: Codon change from HGVS.c notation
... When I wrote "convert it in different ways" I meant "without VEP", because I guess SnpEff doesn't use VEP. I didn't want to use VEP, because I have a lot of data and I don't know the VEP server how much would appreciate me if I send 1000 request per sec. ...
written 3.7 years ago by asd10
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Comment: C: Codon change from HGVS.c notation
... Thank you for your reply. So using a [DNA codon table][1] am I able to convert the HGVS.p to codon change? Are the existing tools for that in R? [1]: https://en.wikipedia.org/wiki/DNA_codon_table ...
written 3.7 years ago by asd10
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Codon change from HGVS.c notation
... The new version of SnpEff changed the original EFF annotation standard to ANN. The EFF field in the VCF contained the codon change which occured in the cancer sample. The new ANN filed just contains the HGVS.c variant notation. The new version of SnpEff statistic HTML file has a codon change table, ...
codon snp sequencing written 3.7 years ago by asd10

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