User: Deniz

gravatar for Deniz
Deniz140
Reputation:
140
Status:
Trusted
Location:
Cambridge
Website:
http://twitter.com/#!/...
Last seen:
4 years, 4 months ago
Joined:
8 years, 8 months ago
Email:
d*********@gmail.com

Mathematician, Biologist.

Posts by Deniz

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Haplotypes For Each Sample
... Hi, What format is your data in? ...
written 6.9 years ago by Deniz140
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Answer: A: Error In Reference Genome
... Although I do not have a good answer, perhaps the following is helpful: The updated mouse reference paper (2007, Plos Biology) might have more information and statistics on this. One way to figure it out would be to sequence many other mice, and then to find which SNPs are unique to the refere ...
written 6.9 years ago by Deniz140
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Data(Base) For Gene Annotations/Models That Include Alternative Splicing For Human?
... I'm aware of the gencode annotation, and RefSeq annotation. Those do a good job at providing gene annotations & models, showing where all the known exons / introns are. In practice, these types of annotations often mean presenting for each gene: a collection of intervals that go together to f ...
splicing database transcription written 7.0 years ago by Deniz140 • updated 7.0 years ago by cdsouthan1.8k
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Answer: A: Why Does Vcf Aggregate Indels Like This?
... This relates to how 1000G is handling MNPs and Complex Variants in VCF; essentially if variants are contiguous or overlap, they're aggregated & the whole thing is treated as one block, as is in the last aggregation example in your question. Also from the spec: Note that in VCF records, t ...
written 7.4 years ago by Deniz140
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Answer: A: Bigger Sample Sizes For Wgs Exome. Is Nosql The Way To Go? Or Bio Hdf
... A FastQ file in a NoSQL database takes more space than a flat fastq.gz file. "Big Data Analytics" is just a buzzword, it doesn't mean anything. NGS has a lot more data than most so-called "big data" applications. How does NoSQL simplify access to data? Now one needs to have a database travellin ...
written 7.4 years ago by Deniz140
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Comment: C: Where Can I Download Vcf Files For Publicly Available Data?
... @zev.kronenberg thanks Zev, my email is denizkural --@T-- gmail --D0T-- com I likewise finally returned to the thread, if a bit late. ...
written 7.5 years ago by Deniz140
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Comment: C: How Do I Convert Fa Files To Bed Format?
... @michael my guess would be that it is due to a confusion of formats & their purposes. happens to the best! ...
written 7.6 years ago by Deniz140
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Comment: C: Where Can I Download Vcf Files For Publicly Available Data?
... Hi Zev -- I'd love to have access to the 200 Danish exomes as well, would be glad to provide more details. ...
written 7.6 years ago by Deniz140
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Answer: A: Where Can I Download Vcf Files For Publicly Available Data?
... VCF is a very flexible format & I would be careful converting Complete Genomics directly into VCF on your own -- for example Complete handles complex variants very differently compared to how 1000G handled them in the Pilot phase. Digging into the supplemental information on the Korean genome pu ...
written 7.6 years ago by Deniz140
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Answer: A: Determining Which New Snps In 1000G Data Result In Coding Changes
... A good way to do it would be to parse the VCF files provided at the 1000 genomes website, and use the fields provided inside the files to filter according to your needs. ...
written 8.7 years ago by Deniz140

Latest awards to Deniz

Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Bigger Sample Sizes For Wgs Exome. Is Nosql The Way To Go? Or Bio Hdf
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Why Does Vcf Aggregate Indels Like This?

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