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User: Scott

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Scott • 80
Reputation:
80
Status:
Trusted
Location:
Canada
Last seen:
1 year, 4 months ago
Joined:
6 years, 4 months ago
Email:
s******@uwo.ca

Posts by Scott

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Ensembl variation ancestral allele data
... This would be okay, but I really need hg38. Ensembl has this in various formats, but if the files in question are FASTA files, it would be very convenient. Thanks! ...
written 2.1 years ago by Scott • 80
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Ensembl variation ancestral allele data
... Hi. I am looking to download ancestral allele data for human. Ensembl has a link on their FTP page (http://useast.ensembl.org/info/data/ftp/index.html) under comparative genomics called "Ancestral Alleles" but it appears to be dead. I would be interested in knowing if these files are still there and ...
ancestral snp ensembl written 2.1 years ago by Scott • 80 • updated 2.1 years ago by Emily_Ensembl ♦ 21k
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Comment: C: Looking for human reference genome with ancestral SNP alleles
... Sounds good. Thanks for the details. Appreciate it! ...
written 2.1 years ago by Scott • 80
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Comment: C: Looking for human reference genome with ancestral SNP alleles
... Thanks, Emily! This is roughly what I thought. I just wasn't sure if any work had gone into individual reference allele re-assignment based on SNP data in more recent builds such as hg38. ...
written 2.1 years ago by Scott • 80
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Looking for human reference genome with ancestral SNP alleles
... Hi. I am looking for reference human genome fasta files (preferably hg38) where the SNP alleles contributing to the reference sequence are always the ancestral alleles, not the "reference" alleles. Any insight into how reference alleles are assigned or became the reference alleles would also be appr ...
genome assembly hg38 snp ensembl written 2.1 years ago by Scott • 80 • updated 18 months ago by kevin.esoh • 0
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Comment: C: HTTP 400 error for select SNPs when using Ensembl Linkage Disequilibrium calcula
... Thank you very much! ...
written 2.1 years ago by Scott • 80
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Comment: C: HTTP 400 error for select SNPs when using Ensembl Linkage Disequilibrium calcula
... Okay thanks. These are just a few examples. I expect to encounter dozens or a few hundred of these cases in my data set... Is there any way to obtain a list of SNPs (perhaps above a certain MAF threshold) that the LD calculator can handle, so that I can filter my list against them before LD calculat ...
written 2.2 years ago by Scott • 80
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HTTP 400 error for select SNPs when using Ensembl Linkage Disequilibrium calculator
... Does anyone know why some SNPs return an error in the Ensembl LD calculator? Example SNPs include rs507666 and rs10423754. They appear to be valid SNP accessions in dbSNP but return an error in the calculator. When accessing programatically it is an HTTP 400; on the web interface it is "AJAX error - ...
ensembl snp ld written 2.2 years ago by Scott • 80 • updated 2.2 years ago by Emily_Ensembl ♦ 21k
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Comment: C: Correct for confounding variable (variability in knockdown efficiency) in paired
... No. One sample has been treated with control shRNA and another sample treated with target shRNA. They are treated in parallel though, hence the pairing. Hope that makes sense. ...
written 3.0 years ago by Scott • 80
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Correct for confounding variable (variability in knockdown efficiency) in paired t-test for change in gene expression
... This is primarily a statistics question, but the biological context may help frame the problem. There are two samples treated with different shRNAs. 1 = control shRNA, 2 = target shRNA. Then PCR is performed on several other (non-target) genes of interest. Several genes change in expression betwe ...
t-test gene ancova qpcr statistics written 3.0 years ago by Scott • 80 • updated 3.0 years ago by Devon Ryan ♦ 98k

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