User: Katie D'Aco

gravatar for Katie D'Aco
Katie D'Aco960
Reputation:
960
Status:
Trusted
Location:
Massachusetts
Twitter:
katiedaco
Last seen:
8 months ago
Joined:
3 years, 7 months ago
Email:
k********@gmail.com

about me

Posts by Katie D'Aco

<prev • 76 results • page 1 of 8 • next >
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Answer: A: Variant Allele Frequency from Ion Torrent data
... The fields FPD and FAO are after correcting for flow order of nucleotides, and so should be more accurate. From https://ionreporter.thermofisher.com/ionreporter/help/GUID-A6D3AE1A-84C6-4B66-AA0D-69244576D2FE.html it looks like they don't use FPD in their allele freq calculations: "AF=FAO/(FAO+FRO) ...
written 2.1 years ago by Katie D'Aco960
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Comment: C: For the general public seeking advice from this community
... Ah, I misunderstood. That just points to how unhelpful and unwelcoming we were, and makes a greater case for a common resource to point people to. ...
written 2.2 years ago by Katie D'Aco960
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Answer: A: For the general public seeking advice from this community
... This was the first of these posts that I've seen on Biostars, but if this isn't a one time thing, then I 100% agree that we should have a post to point them to with more appropriate resources, and also explaining why we as bioinformaticians can't/shouldn't just 'dig in' to their sequencing data (wit ...
written 2.2 years ago by Katie D'Aco960
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Answer: A: HLA-DRB1 variant name description
... I find this site a great reference for understanding HLA naming conventions http://hla.alleles.org/nomenclature/naming.html ...
written 2.2 years ago by Katie D'Aco960
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Answer: A: Large-scale open-source bioinformatics datasets
... BioGPS is a good one for expression data ...
written 2.2 years ago by Katie D'Aco960
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Answer: A: Intersect multiple bed and keep all fields
... Would piping output from intersect to another intersect give you what you want? bedtools intersect -wao -a a.bed -b b.bed | bedtools intersect -wao -a - -b c.bed chr1    10      20      a1      1       +       .       -1      -1      .       -1      .       0       chr1    0  100      c1      1    ...
written 2.3 years ago by Katie D'Aco960
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Comment: C: Getting Population Specific Allele Frequency For Illumina Genotyping Data
... I think 1000 genomes frequencies would be fine to use here. ...
written 2.7 years ago by Katie D'Aco960
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Answer: A: How to draw the distribution of mutation like this?
... Similar Question: https://www.biostars.org/p/61049/ from that thread, this tool might be useful: http://www.cbioportal.org/mutation_mapper.jsp ...
written 2.8 years ago by Katie D'Aco960
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Answer: A: 1000 Genome Project and ESP for indel or frameshift
... What about the ExAc exome browser? It seems to include indels (eg, http://exac.broadinstitute.org/variant/17-41197801-T-TC), and the complete dataset is available for download as a vcf. http://exac.broadinstitute.org/ ...
written 2.9 years ago by Katie D'Aco960
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Comment: C: Mission Impossible: you have 1 minute to analyze the Ebola Genome
... What's really impressive about this is the power behind such basic and standard tools. btw, I found a bug. the last few lines should read:  echo "*** WARNING! The data will self destruct in one minute! ***" echo sleep 60 rm -r ~/edu/mission ...
written 3.0 years ago by Katie D'Aco960 • updated 3.0 years ago by Istvan Albert ♦♦ 74k

Latest awards to Katie D'Aco

Popular Question 21 months ago, created a question with more than 1,000 views. For Back-filling missing genotypes in merged VCF
Popular Question 21 months ago, created a question with more than 1,000 views. For QC Sequence Data from VCF
Teacher 21 months 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 21 months ago, created a question with more than 1,000 views. For Back-filling missing genotypes in merged VCF
Popular Question 22 months ago, created a question with more than 1,000 views. For Allele Frequency Calculator from 1000 Genomes Project
Scholar 2.1 years ago, created an answer that has been accepted. For A: Question about dbSNP rs #s
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Good Answer 2.7 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 2.8 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Scholar 3.2 years ago, created an answer that has been accepted. For A: small case-control exome sequencing study
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Supporter 3.4 years ago, voted at least 25 times.
Scholar 3.4 years ago, created an answer that has been accepted. For A: small case-control exome sequencing study
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Good Answer 3.6 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 3.6 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: How to identify Gene IDs ?
Commentator 3.6 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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