User: onemoreuser
onemoreuser • 20
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Posts by onemoreuser
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Answer:
A: Problem with .vcf annovar
... Did you try Ensembl VEP online?
It´s easy to use and you get MAF as output by default. ...
written 17 months ago by
onemoreuser • 20
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Comment:
C: Co-occuring mutations analysis
... I'm sorry. Yes in the context of cancer: a tool/database that contains information of the effect that multiple variants will have on the patient disease instead of predicting the consequence for independent variants (like ANNOVAR and VEP). ...
written 2.5 years ago by
onemoreuser • 20
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... Is there any software that analysis co-occuring mutations in the dna? Or any database where I can find this type of data? ...
written 2.5 years ago by
onemoreuser • 20
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... Is it correct to use SurfR to analyze intronic variants (from an exome sequencing)? ...
written 2.5 years ago by
onemoreuser • 20
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... GWAVA looks like a good tool to the prediction of the functional impact of non-coding genetic variants (http://www.sanger.ac.uk/science/tools/gwava). But in In the documentation it only mentions support for GRCh37.
Does anyone know if there is support for GRCh38? (I tried to send an email to the GWA ...
written 2.6 years ago by
onemoreuser • 20
• updated
2.5 years ago by
Biostar ♦♦ 20
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... Hi,
I have a TAB file containing somatic and germline variants from RNA sequencing data.
Using tools like: VEP, ANNOVAR or SNPEff, I can annotate the variants but these tools predict the impact variant by variant. They don't consider that different variants interact with each other and one can comp ...
written 2.8 years ago by
onemoreuser • 20
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... I'm reading papers about the phenomenon transition/transversion but there is something that I don't understand. How are these two phenomena represented in literature?
For instance, one paper has "C:G -> T:A" and I can't figure if it is a transition (C->G and T->A) or a transversion (Cs and ...
written 3.5 years ago by
onemoreuser • 20
• updated
3.5 years ago by
Devon Ryan ♦ 96k
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... I run the cuffdiff tool for the first time. My input was something like this:
> cuffdiff -p 5 -o ouput_directory -b reference.fa -L A1,A2 -u
> merged.gtf A1_rep1,A1_rep2 A2_rep1,A2_rep2
Now I'm looking at file "gene_exp.diff" and cufflinks added a 'cufflinks id' for the genes and the transcr ...
written 3.6 years ago by
onemoreuser • 20
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... I searched in ClinVar documentation but I didn't find anything that explains what means a clinical significance "association". The variant is associated with a condition, right? But does it say if it's pathogenic or benign? ...
written 4.1 years ago by
onemoreuser • 20
• updated
4.1 years ago by
Denise CS • 5.1k
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... I don't understand what are the reference and the alternative alleles in the vcf file format. Having a variant with reference='A' and alternative allele='C' and a genotype='0/0' means that the individual is 'A/A'? But in this case how the 'C' was found if the reference is 'A' and the individual is ' ...
written 4.1 years ago by
onemoreuser • 20
• updated
2.2 years ago by
waakurugu.akurugu • 0
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