Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao14k
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Email:
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

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Comment: C: What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it
... I was referring to the library prep actually. Maybe a dense clump of extracted RNA from many cells confers some kind of protection against loss vs less molecules from a single cell. I have no evidence for this at all. And I am sure people more experienced with labwork can correct me. I am just throw ...
written 4 weeks ago by Damian Kao14k
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Answer: A: What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it
... I think the simple answer might just be that handling small amount of molecules is difficult and there is more percentage molecule loss in single cell prep than in percentage loss in bulk. Maybe there is a big difference in how our prep reagents work on the micro-environments of small number of mo ...
written 4 weeks ago by Damian Kao14k
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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 9 weeks 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 10 weeks 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 10 weeks 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 weeks 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 12 weeks 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 6 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 6 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 6 months ago by Damian Kao14k

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Popular Question 4 days ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Popular Question 21 days ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Popular Question 4 weeks ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
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Scholar 10 weeks ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
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: Deseq Sizefactors Help
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 6 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
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 Converting Solid To Srf
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Appreciated 7 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 7 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 7 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Deseq Sizefactors Help
Popular Question 10 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
Popular Question 10 months ago, created a question with more than 1,000 views. For Evolutionary Distance Among Species For Orthology Analysis
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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Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 15 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 15 months ago, created a question with more than 1,000 views. For contigs and scaffolds in abyss
Student 16 months ago, asked a question with at least 3 up-votes. For Communicating With Non-Computational Biologists

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