Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao14k
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UK
Website:
http://blog.nextgeneti...
Last seen:
36 minutes ago
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5 years, 5 months ago
Email:
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Post-doctoral bioinformatician at University of Oxford

Posts by Damian Kao

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Answer: A: StackExchange/Area51 bioinformatics is back
... I think the main problem people have with BioStar boils down to an identity crisis. Is BioStar a Q and A site or a forum? A Q and A type site requires the question to be technical and precise. If someone asks how to convert a format to another format, that can be easily answered. But if someone ...
written 3 days ago by Damian Kao14k
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Comment: C: StackExchange/Area51 bioinformatics is back
... I completely agree with this. I started my phd as the only bioinformatics student in a molecular lab. Biostars was extremely helpful in not just in answering my questions, but also in expanding my knowledge. I learned tons from reading questions/answers that have no relevance to my phd. I don't see ...
written 4 days ago by Damian Kao14k
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Comment: C: Abyss path subprograms
... Thanks for the reply. So the k parameter essentially just let's you specify how long of an overlap you want to consider in building the graph. In the case of AdjList, I guess I'll just set it the same as the -m parameter. So far all the down-stream programs I've tried are working with the SGA unit ...
written 6 days ago by Damian Kao14k
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Abyss path subprograms
... How is the k-mer length used after the initial unitig step in Abyss? Isn't the k-mer length only really relevant in the debruijn unitig assembly step? I want to input unitigs that I generated from SGA and use them for the downstream Abyss steps (AdjList, filtergraph, MergeContigs, etc). Specificall ...
abyss written 7 days ago by Damian Kao14k • updated 6 days ago by benv380
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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 11 weeks ago by Damian Kao14k
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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 11 weeks ago by Damian Kao14k
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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 3 months ago by Damian Kao14k
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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 4 months ago by Damian Kao14k
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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 4 months ago by Damian Kao14k
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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 4 months ago by Damian Kao14k

Latest awards to Damian Kao

Appreciated 1 day ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 3 days 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
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Popular Question 3 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Popular Question 3 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Teacher 5 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 6 months ago, created an answer that was upvoted at least 5 times. For A: Fastqc Html Report To Pdf (With A Script)
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 7 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 8 months ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
Student 9 months ago, asked a question with at least 3 up-votes. For Communicating With Non-Computational Biologists
Appreciated 9 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
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 10 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Popular Question 10 months ago, created a question with more than 1,000 views. For A Chat With Oxford Nanopore’S Clive Brown At Agbt 2013
Teacher 10 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 10 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Scholar 12 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Teacher 12 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 12 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 12 months ago, created a question with more than 1,000 views. For A Chat With Oxford Nanopore’S Clive Brown At Agbt 2013
Appreciated 12 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics

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