User: onemoreuser

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onemoreuser10
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Posts by onemoreuser

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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 8 months ago by onemoreuser10
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Co-occuring mutations analysis
... Is there any software that analysis co-occuring mutations in the dna? Or any database where I can find this type of data? ...
ngs mutations dna written 8 months ago by onemoreuser10
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Comment: A: pathogenicity predictors of cancer mutations
... Is it correct to use SurfR to analyze intronic variants (from an exome sequencing)? ...
written 8 months ago by onemoreuser10
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GWAVA prediction for noncoding variants
... 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 ...
gwava dna prediction tool noncoding written 9 months ago by onemoreuser10 • updated 8 months ago by Biostar ♦♦ 20
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Annotation of genomic variants
... 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 ...
indel analysis mutations snp variants written 12 months ago by onemoreuser10
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Transitions and Transversions representation
... 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 ...
transitions transversions dna written 20 months ago by onemoreuser10 • updated 20 months ago by Devon Ryan86k
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Cuffdiff ouput gene expression data
... 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 ...
cufflinks gene expression cuffdiff rna-seq written 21 months ago by onemoreuser10
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Clinical significance ClinVar
... 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? ...
clinvar clinical significance written 2.3 years ago by onemoreuser10 • updated 2.3 years ago by Denise - Open Targets4.7k
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VCF reference and alternative allele
... 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 ' ...
vcf genome genotype sequencing written 2.3 years ago by onemoreuser10 • updated 4 months ago by waakurugu.akurugu0
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Polymorphism and SNPs
... This is a theory question. I want to know the difference between a Single Nucleotide Polymorphism and a Polymorphism. They are not exactly the same thing but I can't understand the difference. SNP is a single nucleotide change that occurs in a population with a frequency >=1% (by the conventional ...
polymorphism genetics snp written 2.5 years ago by onemoreuser10 • updated 2.5 years ago by Denise - Open Targets4.7k

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