User: Gingi

gravatar for Gingi
Gingi330
Reputation:
330
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Trusted
Location:
Irvington, NY
Website:
http://twitter.com/gingi0
Last seen:
1 year, 2 months ago
Joined:
9 years ago
Email:
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BLAST monkey.

Posts by Gingi

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Github Workflow For Bioinformatics Analysis
... For duplicating your own repository, you can try this. ...
written 6.3 years ago by Gingi330
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Comment: C: Github Workflow For Bioinformatics Analysis
... I would add a git tag too because the question is relevant for generic (non-Github) workflows. (I'm not authorized to edit questions.) ...
written 6.3 years ago by Gingi330
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Comment: C: Github Workflow For Bioinformatics Analysis
... Okay, I missed the essence of the primary question. I'm modifying my answer to accommodate. ...
written 6.3 years ago by Gingi330
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Comment: C: Github Workflow For Bioinformatics Analysis
... You can also attach a top-level Makefile which builds each of the dependent applications/submodules, and even include a target for updating their sources using the git submodule command. This way you only need to recompile when sources change rather than have to manually examine each submodule. ...
written 6.3 years ago by Gingi330
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Answer: A: Github Workflow For Bioinformatics Analysis
... For the first question, you can maintain a basic template repository with a certain directory structure and all the associated software dependencies. You can then use a Github fork to instantiate it duplicate it as another repository, or you can just set the template repository as an additional upst ...
written 6.3 years ago by Gingi330
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Answer: A: Blast Runs In Unix Shell But Not Perl
... The path for blastn might not be set within Perl. For security reasons, it's also usually a bad practice to make system calls to non-builtins without the path being defined (but not necessarily hardcoded). Try hardcoding the path to blastn to see if that at least executes. ...
written 7.3 years ago by Gingi330
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Comment: C: Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
... Thanks, those papers are useful. The SOAPdenovo paper (second link) mentions using step-wise insert sizes "to avoid interleaving," which might be one — if not the primary — reason for using multiple insert sizes. But they don't explore that any further. ...
written 9.0 years ago by Gingi330
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Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
... It's widely accepted that, pound for pound, using multiple short-read libraries with different insert sizes is more effective than a single insert size library for the generation of a _de novo_ assembly of short whole genome shotgun (WGS) reads. Is there a coherent, intuitive explanation why that is ...
assembly next-gen sequencing written 9.0 years ago by Gingi330 • updated 6.3 years ago by Buttonwood40
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Comment: C: Genome Assembly With Physical Map
... I'm grappling with a similar problem, although we are using other mapping resources such as synteny and a genetic linkage map to anchor the contigs to a genome. Other than BAMBUS, I'm not sure there is any turnkey application that can do this effectively. The BAMBUS manual (http://goo.gl/xA5OR) does ...
written 9.0 years ago by Gingi330
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Comment: C: Genome Assembly With Physical Map
... I'm grappling with a similar problem, although we are using other mapping resources such as synteny and a genetic linkage map to anchor the contigs to a genome. Other than BAMBUS, I'm not sure there is any turnkey application that can do this effectively. The [?]BAMBUS manual[?] does handle other [b ...
written 9.0 years ago by Gingi330

Latest awards to Gingi

Good Answer 6.3 years ago, created an answer that was upvoted at least 5 times. For A: Github Workflow For Bioinformatics Analysis
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Github Workflow For Bioinformatics Analysis
Appreciated 6.3 years ago, created a post with more than 5 votes. For A: Github Workflow For Bioinformatics Analysis
Popular Question 9.0 years ago, created a question with more than 1,000 views. For Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
Student 9.0 years ago, asked a question with at least 3 up-votes. For Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
Appreciated 9.0 years ago, created a post with more than 5 votes. For Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
Good Question 9.0 years ago, asked a question that was upvoted at least 5 times. For Why Are Multiple Insert-Size Libraries More Effective In De Novo Assembly?
Teacher 9.0 years ago, created an answer with at least 3 up-votes. For A: Genomic Dna Hash Tables And Ambiguous Bases
Good Answer 9.0 years ago, created an answer that was upvoted at least 5 times. For A: Application Of "Vertex Cover" In Bioinformatics Problems
Teacher 9.0 years ago, created an answer with at least 3 up-votes. For A: Application Of "Vertex Cover" In Bioinformatics Problems
Appreciated 9.0 years ago, created a post with more than 5 votes. For A: Application Of "Vertex Cover" In Bioinformatics Problems

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