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User: samesense

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samesense • 40
Reputation:
40
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New User
Location:
United States
Last seen:
6 months, 2 weeks ago
Joined:
5 years, 11 months ago
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s********@gmail.com

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Posts by samesense

<prev • 8 results • page 1 of 1 • next >
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Answer: A: fastq-dump timeout exhausted error
... 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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Comment: C: Indexing Compressed Fastq-Like Data
... [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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Comment: C: fastSTRUCTURE failing to cluster one thousand genomes south asians
... 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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Comment: C: Snakemake: set cluster cores per rule
... 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
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fastSTRUCTURE failing to cluster one thousand genomes south asians
... 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 ...
ancestry faststructure plink gwas written 3.2 years ago by samesense • 40 • updated 3.2 years ago by Brice Sarver • 2.4k
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Comment: C: Snakemake: set cluster cores per rule
... 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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Snakemake: set cluster cores per rule
... 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 ...
snakemake written 3.4 years ago by samesense • 40 • updated 3.4 years ago by maciek.kandula • 0
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Database Of Structurally Derived Protein Features
... 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 ( ...
database uniprot written 4.0 years ago by samesense • 40 • updated 3.8 years ago by ddofer • 30

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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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