User: Katie D'Aco

gravatar for Katie D'Aco
Katie D'Aco1000
Reputation:
1,000
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Trusted
Location:
Massachusetts
Twitter:
katiedaco
Last seen:
3 years ago
Joined:
5 years, 12 months ago
Email:
k********@gmail.com

about me

Posts by Katie D'Aco

<prev • 76 results • page 2 of 8 • next >
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Answer: A: How many of the human reference sequence alleles are derived alleles?
... Check out the paper Initial sequence of the chimpanzee genome and comparison with the human genome it might have what you're looking for. From the first page:  "Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome, with 1.06% or less corres ...
written 5.4 years ago by Katie D'Aco1000
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Comment: C: Back-filling missing genotypes in merged VCF
... Excellent! I had to think for a minute about how "correct" only using read depth is to decipher ./. from 0/0, but we also know that there was originally no variant called at that location. So it will generally be pretty accurate. Looking forward to trying this tool. ...
written 5.4 years ago by Katie D'Aco1000
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Back-filling missing genotypes in merged VCF
... Is there a good way to distinguish ./. from 0/0 in a merged vcf? For example, a tool that goes back to the bam files for missing genotypes and checks if it's homozygous reference or a NO CALL? I would imagine this would be important to do, especially in 30x WGS where there are a lot of low coverage ...
vcf written 5.4 years ago by Katie D'Aco1000 • updated 3.9 years ago by Biostar ♦♦ 20
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Comment: C: What bioinformatics tools/software do not get enough recognition?
... Can we make this happen? Maybe I'm naive, but I feel like it would be feasible to raise $5,000 from personal and corporate contributions for a widely loved, under funded tool. ...
written 5.4 years ago by Katie D'Aco1000
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Answer: A: universally heterozygous "SNP" in geuvadis VCF?
... Yes, this is relatively common, and it is usually related to misalignment of the reads, especially when there are pseudogenes for the region the reads were mapped to. I assume snp_1_145075854 is at chr1:145075854, which maps to the gene PDE4DIP, which has 7 known pseudogenes (see http://www.ncbi.nlm ...
written 5.4 years ago by Katie D'Aco1000
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Comment: C: Public Disease Exomes (VCF)
... Devon, the ExAC exomes are not annotated with phenotypes, but they do include samples from disease cohorts, so your idea of searching for samples with known disease mutations is a good one. ...
written 5.5 years ago by Katie D'Aco1000
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Comment: C: combining sequencing variants
... I've used EIGENSTRAT to do PCA, but there are other tools that do this. If you plot your subjects along the first 2 PCs and they are clustered by sequencing technology then you don't want to use the combined data set to do association tests.  Before you do PCA you want to do LD-pruning (can be done ...
written 5.6 years ago by Katie D'Aco1000
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Answer: A: combining sequencing variants
... You should first normalize the variants if they aren't already. Then use a combination of bedtools intersect (to get the regions where the targets from the two projects overlap) and vcftools merge (to combine the vcf's from the two projects into a single vcf).  Before doing any association tests, do ...
written 5.6 years ago by Katie D'Aco1000
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Answer: A: Question about dbSNP rs #s
... rsID's will stay the same from genome build to genome build, even if the genomic coordinates change. The one gotcha to your plan I can think of is if the rsID was removed from dbSNP or merged with another rsID. ...
written 5.6 years ago by Katie D'Aco1000
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Comment: C: Template-specific primers design
... I think primer3 uses a heuristic to estimate genome wide specificity (could be wrong about that). Have you seen PRIMEGENS? Not sure how it works, but it looks like it takes a reference sequence as a parameter. ...
written 5.6 years ago by Katie D'Aco1000

Latest awards to Katie D'Aco

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Back-filling missing genotypes in merged VCF
Popular Question 4.1 years ago, created a question with more than 1,000 views. For QC Sequence Data from VCF
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Ideas or advise for data visualization that shows genotype and phenotpye relatio
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Back-filling missing genotypes in merged VCF
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Allele Frequency Calculator from 1000 Genomes Project
Scholar 4.5 years ago, created an answer that has been accepted. For A: Question about dbSNP rs #s
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Ideas or advise for data visualization that shows genotype and phenotpye relatio
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Scholar 5.6 years ago, created an answer that has been accepted. For A: small case-control exome sequencing study
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Supporter 5.8 years ago, voted at least 25 times.
Scholar 5.8 years ago, created an answer that has been accepted. For A: small case-control exome sequencing study
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Good Answer 5.9 years ago, created an answer that was upvoted at least 5 times. For A: Ideas or advise for data visualization that shows genotype and phenotpye relatio
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Commentator 6.0 years ago, created a comment with at least 3 up-votes. For C: What's the correct way to withdraw a published database/server ?

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