User: Eugene A

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Eugene A80
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Posts by Eugene A

<prev • 33 results • page 1 of 4 • next >
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Answer: A: Gnomad genome vs Gnomad exom (extremely rare Ref case)
... So I eventually figure out the answer, with a help from gihub (https://github.com/broadinstitute/gnomad-browser/issues/602) and will briefly explain it here: There is a sequence change between GRCh37 and GRCh38 in the position of interest: AGGCTT - GRCCh37 AGGGCTT - GRCh38 Therefore what ...
written 3 days ago by Eugene A80
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Comment: C: Gnomad genome vs Gnomad exom (extremely rare Ref case)
... Hi, yes, I did drop an email to Gnomad contact adress couple of days ago but still waitig for the response ...
written 10 days ago by Eugene A80
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Comment: C: Understanding VCF : 0/0 v 0/1 v 1/0 v 1/1 etc
... Not sure what do you mean by "significance", it is just notation for genotype (as far as you do have 2 copie of DNA in each cell). So both copies of the DNA in your example harbour reference variant which is C. If the question was: how sure you are about the fact that you do not have a T in this po ...
written 13 days ago by Eugene A80
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Comment: C: Gnomad genome vs Gnomad exom (extremely rare Ref case)
... Hi, thanks for the comment. I do understand that gnomadV3 does not contain exomes. BUT it **must** contain the variant that has frequency of alt allele of AF=9.99979e-01 in gnomadV2 (at least I do not see any reason why not). ...
written 15 days ago by Eugene A80
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Comment: C: ACMG assignment tools
... Thanks - I'll have a look! ...
written 15 days ago by Eugene A80
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Gnomad genome vs Gnomad exom (extremely rare Ref case)
... Hi, I've accidently noticed that an SNP with close to 1 allele frequency in Gnomad exom does not show up in gnomad Genome and that is something that turns out to have a consequence for the automatic ACMG annotation. The SNP is https://www.ncbi.nlm.nih.gov/snp/rs142200057 It has almost zero frequen ...
gnomad snp written 18 days ago by Eugene A80
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Comment: C: ACMG assignment tools
... Which one? InterVar internal db (lists of lof genes etc?) are still the same I have in mind to update these in the future. For cravat you need several available annotators and several custome, which I assembled from open sources (like dbnsfp) ...
written 21 days ago by Eugene A80
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Comment: C: GC content of 10x Genomics
... Thanks! And also R1 is written in fastq in reverse complement to the actual order of sequencing ...
written 5 weeks ago by Eugene A80
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Comment: C: GC content of 10x Genomics
... Yes, a run it through cellRanger, but I want to understand this QC report ;) ...
written 5 weeks ago by Eugene A80
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Comment: C: GC content of 10x Genomics
... I gave it a bit more thoughts and now confused even more ( here is the library pic. from 10x genomic website R1 if I understand corretcly (and seems that I do not), should looks like: 5'-CellBarcode-UMI-polyA-cDNA-3' And R2: 5'-cDNA-polyA(depending on insert size and seq len)-3' In my data I s ...
written 5 weeks ago by Eugene A80

Latest awards to Eugene A

Scholar 3 days ago, created an answer that has been accepted. For A: Gnomad genome vs Gnomad exom (extremely rare Ref case)
Popular Question 23 days ago, created a question with more than 1,000 views. For Individual genes plots after batch correction with Deseq2

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