User: ognjen011

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ognjen011150
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Posts by ognjen011

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Comment: C: Finding SNPs RSID from older papers
... I see what was done. The accession link is actually: https://www.ncbi.nlm.nih.gov/nuccore/AF039228 And it was sequenced from -550-+61. As a result, -174 is not counted from the end of the sequence as I assumed. Unusual. ...
written 2 days ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Hey, I've just found the explicit variant: https://www.snpedia.com/index.php/Rs1800795 The position of this base is 22727026. When counting -174 from the end of your aligned sequence, I get a position 22727024. Also, the "real" SNP is C > G. Could you comment on that? ...
written 2 days ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Thanks for the reply. Using BLAST is a great idea. Is there a resource that could help me skip BLAST if the sequence has a known accession number? For example, if I know my variant is NM_001105580:c.1394T>C, how would one skip BLAST and directly get the absolute genomic position in the current bu ...
written 5 days ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Thank you for clearly outlying your reasoning. ...
written 5 days ago by ognjen011150
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Finding SNPs RSID from older papers
... I encountered a paper which test an IL-6 polymorphism, but never clearly specifies it with an RSID, but simply calls it IL-6 -174: https://www.ncbi.nlm.nih.gov/pubmed/18930842 I tried using online resources to find the exact chromosomal position and thus find the RSID that corresponds to position ...
assembly rsid snp written 6 days ago by ognjen011150 • updated 6 days ago by Denise - Open Targets4.7k
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Meaning of TOP/BOTTOM strand and QC implications
... I've found a post explaining strand designations for some Illumina systems: https://www.illumina.com/documents/products/technotes/technote_topbot.pdf So the way they explain it is some local designation which is robust to reference genome build rearrangements. What confuses me is the supplementary ...
illumina snp written 27 days ago by ognjen011150
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Convention for protein-level changes
... I have come to understand that G37 or Gly37 are changes to aminoacid Gly at position 37. I ran into this paper: https://www.nature.com/articles/s41467-017-00257-5 What is PheSerTyr13? ...
protein nomenclature written 7 weeks ago by ognjen011150
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Comment: C: RSID for multiple alternative variants present in a single line
... Thanks for the reply! Can you answer the above question in the comment as well? ...
written 12 weeks ago by ognjen011150
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Comment: A: RSID for multiple alternative variants present in a single line
... Thanks for your reply, I didn't expect that but I see examples of it when I look through dbSNP. Does that mean a variant in dbSNP can be uniquely identified by {chr:pos_ref}? What about indels? Are they all bundled together as long as the position is the same or is this more complex? ...
written 12 weeks ago by ognjen011150
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RSID for multiple alternative variants present in a single line
... How does assigning RSID (dbsnp IDs) work when there are multiple variants at the same line? For example, if the genotype is 1/2, and of of these variants have a distinct RSID, would they both be assigned, separated by comma? And what about multi-sample VCFs, is the situation the same (e.g. 0/1 and 0 ...
vcf rsid genotype written 12 weeks ago by ognjen011150

Latest awards to ognjen011

Supporter 27 days ago, voted at least 25 times.
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Good Question 15 months ago, asked a question that was upvoted at least 5 times. For BED files for SRA open projects
Student 15 months ago, asked a question with at least 3 up-votes. For BED files for SRA open projects

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