Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao14k
Reputation:
13,640
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Location:
UK
Website:
http://blog.nextgeneti...
Last seen:
8 hours ago
Joined:
5 years, 6 months ago
Email:
d*********@gmail.com

Post-doctoral bioinformatician at University of Oxford

Posts by Damian Kao

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Comment: C: Eukaryotic Genome Annotation in 2016
... Repeatmasker is used here to prevent augustus from predicting genes in repeat regions. ...
written 17 days ago by Damian Kao14k
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fitting model to a read coverage spectra
... K-mer spectra of genomic reads are usually modeled as a poisson mixture process where each of the components represents the variety of ploidies of a genome. So a k-mer spectra that looks like the following can be interpreted as showing a poisson component representing heterozygous regions (1N) and a ...
genome k-mer spectra read coverage written 22 days ago by Damian Kao14k
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Comment: C: StackExchange/Area51 bioinformatics is back
... I agree with you to a degree about the Q&A format. I think a nicely structured searchable knowledge base would be very helpful and maybe SE can become that. But I also think that the nature of the bioinformatics field probably means there are enough questions of the abstract type which warrant ...
written 24 days ago by Damian Kao14k
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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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks ago by Damian Kao14k • updated 5 weeks ago by benv430
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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 3 months 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 3 months 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 4 months ago by Damian Kao14k

Latest awards to Damian Kao

Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Teacher 28 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
Good Answer 29 days ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Appreciated 29 days ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Converting Solid To Srf
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 5 weeks 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 5 weeks ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Popular Question 4 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Teacher 6 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 7 months ago, created an answer that was upvoted at least 5 times. For A: Fastqc Html Report To Pdf (With A Script)
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 9 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 9 months ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
Student 10 months ago, asked a question with at least 3 up-votes. For Communicating With Non-Computational Biologists
Appreciated 10 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
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
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

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