User: Scott
Scott • 80
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- Canada
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- 1 year, 4 months ago
- Joined:
- 6 years, 4 months ago
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Posts by Scott
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... 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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... 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 ...
written 2.1 years ago by
Scott • 80
• updated
2.1 years ago by
Emily_Ensembl ♦ 21k
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... Sounds good. Thanks for the details. Appreciate it! ...
written 2.1 years ago by
Scott • 80
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... 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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... 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 ...
written 2.1 years ago by
Scott • 80
• updated
18 months ago by
kevin.esoh • 0
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... Thank you very much! ...
written 2.1 years ago by
Scott • 80
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... 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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... 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 - ...
written 2.2 years ago by
Scott • 80
• updated
2.2 years ago by
Emily_Ensembl ♦ 21k
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... 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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... 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 ...
written 3.0 years ago by
Scott • 80
• updated
3.0 years ago by
Devon Ryan ♦ 98k
Latest awards to Scott
Teacher
3.0 years ago,
created an answer with at least 3 up-votes.
For A: remove non biallelic SNPs from ped
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4.6 years ago,
created a question with more than 1,000 views.
For calculating LD for SNPs with more than two alleles
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4.6 years ago,
created a question with more than 1,000 views.
For Problem with Haploview loading of files from latest (Sept 15-17 2014) update to phase 3 release of 1000 Genomes data
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For Linkage disequilibrium analysis of EUR populations from 1000 Genomes phase3 data: Considerations of singletons vs family trios
Popular Question
6.2 years ago,
created a question with more than 1,000 views.
For Linkage disequilibrium analysis of EUR populations from 1000 Genomes phase3 data: Considerations of singletons vs family trios
Popular Question
6.3 years ago,
created a question with more than 1,000 views.
For Problem with Haploview loading of files from latest (Sept 15-17 2014) update to phase 3 release of 1000 Genomes data
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