Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao14k
Reputation:
13,790
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Trusted
Location:
UK
Website:
http://blog.nextgeneti...
Last seen:
10 hours ago
Joined:
5 years, 10 months ago
Email:
d*********@gmail.com

Post-doctoral bioinformatician at University of Oxford

Posts by Damian Kao

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Comment: C: Explanation of very high alignment rate with bowtie2
... I assume the Trinity assembly was not assembled from the reads you are mapping? ...
written 8 days ago by Damian Kao14k
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Comment: C: bowtie2 malformed sam/bam files
... I am actually not sure if 2.3.0 works with 2.3.0 index. I would assume so? The release notes doesn't indicate that a new index should be generated. I'll inform them of the bug. ...
written 9 days ago by Damian Kao14k
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Answer: A: bowtie2 malformed sam/bam files
... After dealing with this for several hours I realized the problem is with my bowtie2 index. I generated my index with bowtie2 2.3.0. It looks like mapping with 2.3.3 on a 2.3.0 index is causing these problems. ...
written 9 days ago by Damian Kao14k
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bowtie2 malformed sam/bam files
... Does anyone have any experience with bowtie2 (2.3.3) generating malformed sam/bam files? I am mapping a set of fasta files (not fastq) to a set of transcriptome sequences. I noticed from my .sam output that there were a lot of malformed entries. I wrote a quick script to pull some of these lines o ...
bowtie2 mapping written 10 days ago by Damian Kao14k
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... I am by no means an expert in this field, but are there any similarities between the network propagation based algorithm to the MCL clustering algorithm? Both seems to be weighing nodes based on probable walk distances? ...
written 28 days ago by Damian Kao14k
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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 4 months 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 4 months 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 4 months 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 months 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 months ago by Damian Kao14k

Latest awards to Damian Kao

Scholar 14 days ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Teacher 3 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 4 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
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 4 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Appreciated 4 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 4 months ago, created a question with more than 1,000 views. For Converting Solid To Srf
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Appreciated 5 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Popular Question 8 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
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
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Fastqc Html Report To Pdf (With A Script)
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 12 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 13 months ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
Student 14 months ago, asked a question with at least 3 up-votes. For Communicating With Non-Computational Biologists
Appreciated 14 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field

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