Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao13k
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Location:
UK
Website:
http://blog.nextgeneti...
Last seen:
2 hours ago
Joined:
5 years, 4 months ago
Email:
d*********@gmail.com

Post-doctoral bioinformatician at University of Oxford

Posts by Damian Kao

<prev • 838 results • page 1 of 84 • next >
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Comment: C: specifying chromosome sizes and output with bedGraphToBigWig
... The error sounds like there is a string somewhere in your files (bedgraph or genome file) where there is supposed to be a integer. Try grepping for "size" in either files. ...
written 6 weeks ago by Damian Kao13k
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Comment: C: MinHash Sketch - A Tool for Rapid Sequence Comparison
... Nice. I think this is how miniasm does it's alignments also? ...
written 7 weeks ago by Damian Kao13k
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Comment: C: In this Python script I want to save result of print(traj_rmsd) in an output.xv
... You are writing it as a binary file ('wb'). Is that what you wanted to do? If you want to open it as text, just use 'w' instead of 'wb'. ...
written 9 weeks ago by Damian Kao13k
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Comment: C: What is the most rational way and technology to write your own web-interface to
... Is the point being able to access the tools from the web or having a user friendly UI? If it's just for the former, you can just use some kind of web-terminal interface (http://guacamole.incubator.apache.org/). If you want a user friendly UI that non-computational people can use, then I would just ...
written 3 months ago by Damian Kao13k
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Comment: C: Eukaryotic Genome Annotation in 2016
... The extrinsic sources are defined in a extrinsic.cfg file somewhere in your augustus directory. You can manually edit their weights or add new sources if you want. You are going to have to play around with the weights. This part can be very subjective. ...
written 3 months ago by Damian Kao13k
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Answer: A: What is "^A" in NR database?
... The website where you downloaded this from says: > If an entry in nr represents multiple source database entries, the > Fasta title lines are concatenated together with CTRL+A as the > delimiter. ^A is same as CTRL+A. I don't think it will influence making a blast database as I think they ...
written 3 months ago by Damian Kao13k
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Answer: A: What is a "draft genome assembly"?
... I am sorry to be pedantic about this, but I think there is a deeper point to be made here about what "completeness" can mean in terms of genome assemblies. All the genome assemblies we have right now for various organisms are really an amalgamation of the individuals/samples/cells that were collec ...
written 4 months ago by Damian Kao13k
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Comment: C: How to efficiently reuse and optimize same code block in wrapper function?
... I'll keep this post open because there is a healthy discussion going on. I enjoy discussing programming issues also, however, this is really more suited to stackexchange as it is tangentially related to bioinformatics. ...
written 4 months ago by Damian Kao13k
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Comment: C: Easy way to automatically save images of Krona HTML charts?
... I've found SVG to be a bit loose as a specification. Different programs can sometimes render differently. I think phantomjs should be able to handle it. So use phantomjs to render the svg and save the "page" as png. I've used phantomjs in the past on d3.js generated svgs successfully. ...
written 4 months ago by Damian Kao13k
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Comment: C: Easy way to automatically save images of Krona HTML charts?
... It looks like the snapshot button calls the snapshot() function js. I think you can get phantomjs to call a function after rendering (I think it was page.evaluate). Then you can probably save the snapshot which is just a svg to file. ...
written 4 months ago by Damian Kao13k

Latest awards to Damian Kao

Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Fastqc Html Report To Pdf (With A Script)
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 6 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 7 months ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
Student 8 months ago, asked a question with at least 3 up-votes. For Communicating With Non-Computational Biologists
Appreciated 8 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Popular Question 9 months ago, created a question with more than 1,000 views. For A Chat With Oxford Nanopore’S Clive Brown At Agbt 2013
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Scholar 9 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Scholar 11 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Appreciated 11 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 11 months ago, created a question with more than 1,000 views. For A Chat With Oxford Nanopore’S Clive Brown At Agbt 2013
Appreciated 11 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Appreciated 11 months ago, created a post with more than 5 votes. For Communicating With Non-Computational Biologists
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Some Questions About Using Orthomcl To Find Orthologs Within Many Species

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