User: samesense
samesense • 40
- Reputation:
- 40
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- United States
- Last seen:
- 6 months, 2 weeks ago
- Joined:
- 5 years, 11 months ago
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about me
Posts by samesense
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... NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as sra-tools, ncbi-vdb or ngs.
If you develop software that relies on sra-tools, n ...
written 7 months ago by
samesense • 40
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... [web archive link][1]
Look for fileindex on April 10, 2010
[1]: https://web.archive.org/web/20130416105924/http://hackmap.blogspot.com/ ...
written 10 months ago by
samesense • 40
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... With k=10, I can place more than half of the SAS samples confidently.
...
written 3.2 years ago by
samesense • 40
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... I tried setting a download resource, according to this answer
https://groups.google.com/forum/#!searchin/snakemake/parallell$20resources/snakemake/PAfWikWvmG4/WAArbq-_ea0J
This did not limit the downloads as expected.
...
written 3.2 years ago by
samesense • 40
1
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1
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... I want to determine the ancestry of 1000 individuals using SNPs from complete genomics whole genome sequencing. I'm using the complete genomics one thousand genomes samples to help assign ancestry into EUR, AFR, ASN, SAS, AMR. As a sanity check, I first run plink and fastSTRUCTURE on only the 1KG sa ...
written 3.2 years ago by
samesense • 40
• updated
3.2 years ago by
Brice Sarver • 2.4k
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... I saw that too. I think it would multithread my download, but wait on the rule to finish before moving onto the downstream pipeline. I'll ask the user group.
...
written 3.3 years ago by
samesense • 40
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1
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1.4k
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... I need to download hundreds of large files, and run each of them through my snakemake pipeline. The file download is fast compared to my downstream pipeline. I'd like to limit the number of parallel downloads to 5, but allow the downsteam processing to use 100 cores. In snakemake, is there a way to ...
written 3.4 years ago by
samesense • 40
• updated
3.4 years ago by
maciek.kandula • 0
4
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1
answer
908
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5 follow
1
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... I have a list of a thousand residues identified on uniprot proteins. I need to gather features of these residues for a classifier. Some features require protein structures. I have a pipeline for finding appropriate structures using the protein model portal, and calculating structure based features ( ...
Latest awards to samesense
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Snakemake: set cluster cores per rule
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For fastSTRUCTURE failing to cluster one thousand genomes south asians
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