User: Nancy Ouyang

gravatar for Nancy Ouyang
Nancy Ouyang170
Reputation:
170
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Trusted
Location:
United States
Last seen:
5 years, 6 months ago
Joined:
6 years ago
Email:
n****@curoverse.com

Posts by Nancy Ouyang

<prev • 20 results • page 1 of 2 • next >
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Comment: C: hg19 vs hg38 in two pictures
... I agree -- I feel like aligning reads to the reference genome is very much a bootstrapping process which gradually gets more and more "true" over time, sort of like how we built more and more precise machining tools over time (or how, if today we personally want bootstrap / build a machine shop from ...
written 5.7 years ago by Nancy Ouyang170
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Comment: C: hg19 vs hg38 in two pictures
... Oh, interesting. There's still a lot of alt-ref-loci that are actually placed on chromosomes, even if you exclude all the ChrUn's -- have you found those to be suspect? For instance, my understanding was that for places like the KIR regions, hg19 smooshed them all into one-ish region, and hg38 inste ...
written 5.7 years ago by Nancy Ouyang170
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hg19 vs hg38 in two pictures
... Took these two screenshots recently, thought you all might enjoy them. Shows our evolving understanding of the complexity of the human genome at the population-scale, as reflected in the changes in the reference genome between hg19 and hg38. (ignore the temp folder, not part of hg19) Note: I m ...
hg38 hg19 written 5.7 years ago by Nancy Ouyang170 • updated 5.7 years ago by Giovanni M Dall'Olio27k
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Comment: C: A global network of millions of genomes could be medicine’s next great advance.
... Hi, any chance the talk is online in video form or summarized somewhere? I'd be interested in hearing more. Thanks! ...
written 5.7 years ago by Nancy Ouyang170
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Comment: C: New to Python. Need help writing a program comparing 2 DNA sequences.
... Hi -- you may appreciate http://rosalind.info/problems/ini/, has some practical example python problems and solutions :) ...
written 5.8 years ago by Nancy Ouyang170
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Comment: C: Arvados vs Big Data Genomics
... Hello! Depends what you're looking for with respect to variant storage and retrieval, but I would like to note that there is already a free hosted version of Arvados that people are welcome to evaluate (you can use any google account to login). disclaimer: I contribute to Arvados. We would definite ...
written 5.9 years ago by Nancy Ouyang170
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Answer: A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
... I like this list, which provides detailed comments on each source and also think about the overall structure. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002632  An Online Bioinformatics Curriculum David B. Searls Published: September 13, 2012   The last sentence o ...
written 6.0 years ago by Nancy Ouyang170
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Comment: C: Retrieve all FASTA RefSeq files for a given entry in NCBI gene?
... I think I have a working solution via https://www.biostars.org/p/122680 parsing the XML of the gene entry -> running efetch with the seq start and end. I'll report back when I get all the steps working together. Thanks for showing me how to work with entrez direct! ...
written 6.0 years ago by Nancy Ouyang170
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Comment: C: Entrez xtract "unrecognized argument '-match'" error
... Thanks for answering my specific question! It's weird their error message says "before" :/ I wasn't sure who to give the checkmark to, but I think Pierre Lindenbaum answered my actual question. ...
written 6.0 years ago by Nancy Ouyang170
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Comment: C: Entrez xtract "unrecognized argument '-match'" error
... Hah, my initial reaction was "what sorcery is this?" Neat, I'd never heard of xslt before. Thanks!   ...
written 6.0 years ago by Nancy Ouyang170

Latest awards to Nancy Ouyang

Student 5.7 years ago, asked a question with at least 3 up-votes. For hg19 vs hg38 in two pictures
Scholar 6.0 years ago, created an answer that has been accepted. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics

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