User: DCGenomics

gravatar for DCGenomics
DCGenomics320
Reputation:
320
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United States
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2 months, 3 weeks ago
Joined:
5 years, 7 months ago
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Posts by DCGenomics

<prev • 36 results • page 1 of 4 • next >
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Comment: C: error while downloading taxonomy using E-utilities
... The user should first do a fresh reinstall of EDirect, most importantly running the "./edirect/setup.sh" command at the end of the installation instructions, in order to get all of the Perl modules properly loaded. Then he should execute the following commands: export NCBI_API_KEY=${redac ...
written 12 weeks ago by DCGenomics320 • updated 12 weeks ago by genomax73k
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Answer: A: Usage of 'xtract'
... Try a fresh download of Entrez Direct. The current version has an xtract wrapper that launches the appropriate precompiled binary, in this case xtract.Linux. Xtract was rewritten two years ago, replacing the original Perl implementation, and now always handles recursive data structures. Thus, the ...
written 23 months ago by DCGenomics320
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Comment: C: entrez utilities: snp
... I have it on good information that if you update your implementation of eutils, this should work fine. ...
written 2.1 years ago by DCGenomics320
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Answer: A: Difference between NCBI Entrez formats (e.g., xml, docsum) for efetch
... Perhaps this will be useful to you: https://github.com/NCBI-Hackathons/EDirectCookbook ...
written 2.5 years ago by DCGenomics320
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Answer: A: Entrez API returns results different from main search?
... Two things, NCBI Education Group has been offering webinars on this lately. Check out some of the recent ones at: https://www.ncbi.nlm.nih.gov/home/coursesandwebinars.shtml Also, if you put in an issue here, we'll try to help you with a solution: https://github.com/NCBI-Hackathons/EDirect_EUt ...
written 2.7 years ago by DCGenomics320
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Answer: A: NCBI NOW (Next generation sequencing Online Workshop) October 13 - 23 , 2015
... Videos available here: https://www.ncbi.nlm.nih.gov/news/11-24-2015-ncbi-now-videos/ ...
written 2.9 years ago by DCGenomics320
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Answer: A: Entrez Direct E-utilities - using match and xtract to filter by data value
... Xtract 5.50, part of today's EDirect release, has better methods for handling recursive objects, with two specific improvements: 1) Nested exploration (e.g., "*/Gene-commentary") masks deeper objects from being seen by the -element selection command. It is no longer necessary to use -first instead ...
written 2.9 years ago by DCGenomics320 • updated 2.9 years ago by genomax73k
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Answer: A: Code for interactive web-based chromosome ideogram viewer?
... This might be worth checking out! https://github.com/NCBI-Hackathons/rnaseqview ...
written 3.0 years ago by DCGenomics320
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News: (Closed) NCBI Resources Developers Forum!
... If you’re a developer who uses NCBI resources, we’d like to hear from you! Details: ...
assembly genome news snp rna-seq blast written 3.1 years ago by DCGenomics320 • updated 3.1 years ago by Michael Dondrup46k
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Answer: A: Entrez direct E-utilities - "efetch" command to retrieve CDS with protein access
... The following EDirect commands will get the CDS FASTA from a protein accession: elink -db protein -id XP_003399879.1 -target nuccore | \ efilter -molecule mrna | \ efetch -format fasta_cds_na ...
written 3.1 years ago by DCGenomics320 • updated 12 months ago by h.mon27k

Latest awards to DCGenomics

Appreciated 3.1 years ago, created a post with more than 5 votes. For A: How can I download the whole ClinVar database
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: How can I download the whole ClinVar database
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted

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