Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao15k
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http://blog.nextgeneti...
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

<prev • 912 results • page 2 of 92 • next >
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Comment: C: Strange Depth of Coverage distribution
... Even if multiple samples were mixed together in the depth of cov reporting, it should not show this distribution. Multi-sample mix should show a smooth histogram with potentially multiple peaks. Maybe try using samtools stats' depth of coverage info for plotting and see if you get the same thing. Pe ...
written 23 months ago by Damian Kao15k
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Comment: C: Strange Depth of Coverage distribution
... This looks like a histogram plotting issue where it is binning the depth values in a skewed way. ...
written 23 months ago by Damian Kao15k
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... I don't think it is possible to differentiate between batch effects and biological effect in this case. If you performed the experiment with biological conditions side by side in two batches, then you can try to look for batch effects. ...
written 2.0 years ago by Damian Kao15k
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Answer: A: Tophat vs Bowtie alignment rates
... As far as I know, Tophat2 uses Bowtie2 in several stages. The initial stages (mapping to transcriptome and genome) are performed to get all the unmapped reads. The unmapped reads are then splitted and mapped separately to check if they span an intron. How bowtie2 is parameterized in Tophat2 is like ...
written 2.0 years ago by Damian Kao15k
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Comment: C: how to count the nucleotide frequency of paired ended fasta files
... Are your fastqs paired in the same order already? Do you have entries where one of the pair (forward or reverse) is missing? ...
written 2.0 years ago by Damian Kao15k
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Comment: C: New to Whole Exome Sequencing and Manhattan Plot and I need to understand how to
... Everyone who participates on this website by answering questions are doing this voluntarily. We do not get paid or benefit from this. We all have other responsibilities in our professional and personal lives. We are not here to act as your professor or full-time teacher. I understand that learning ...
written 2.0 years ago by Damian Kao15k
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Answer: A: Pulling out interval adjoining regions
... As with most interval operations, bedtools has a command for it: https://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 2.3 years ago by Damian Kao15k
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Comment: C: SNP calling from BAM file
... Can you please post the command you used and the error message. ...
written 2.3 years ago by Damian Kao15k
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Answer: C: RNA-seq normalization and standardization
... Packages like edgeR and DESeq2 don't actually transform the counts for DE analysis. A normalization factor is calculated and then used in the DE test. There are good information in the absolute counts for each gene. Standardization is not used, otherwise that information would be lost. ...
written 2.4 years ago by Damian Kao15k
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Comment: C: Abyss run time
... What's the estimated genome size of your organism? And how many reads do you have? ...
written 2.4 years ago by Damian Kao15k

Latest awards to Damian Kao

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
Scholar 6 months ago, created an answer that has been accepted. For C: Does trinity discard reads shorter than 25-mer?
Great Question 8 months ago, created a question with more than 5,000 views. For Chip-seq analysis with input and spike-in
Teacher 8 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
Popular Question 9 months ago, created a question with more than 1,000 views. For Abyss unitigs filtering
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
Great Question 10 months ago, created a question with more than 5,000 views. For Encode Commentary From Dan Graur
Great Question 11 months ago, created a question with more than 5,000 views. For Encode Commentary From Dan Graur
Teacher 13 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
Teacher 15 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
Popular Question 16 months ago, created a question with more than 1,000 views. For Interpreting Trinity components
Popular Question 18 months ago, created a question with more than 1,000 views. For segment duplication vs heterozygosity
Teacher 18 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
Teacher 20 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 21 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 21 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 21 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Scholar 21 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Appreciated 22 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 22 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 23 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Appreciated 23 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 23 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 2.0 years ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
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