Moderator: Dan Gaston

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Dan Gaston7.1k
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Canada
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1 week ago
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7 years, 4 months ago
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Clinical Laboratory Bioinformatician and Assistant Professor. Department of Pathology, Nova Scotia Health Authority and Dalhousie University. Next-generation sequencing-based molecular diagnostics with a focus on cancer genomics and transcriptomics. Genomic analysis of rare Mendelian diseases. Some analysis and work with bacterial and viral genomics. A passion for software development. Particularly web-services, visualization, project-management, and analysis pipelines.

PhD background in phylogenetics and molecular evolution. Focused on functional divergence and subcellular localization, analysis of next-generation sequencing data.

Posts by Dan Gaston

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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... BWA is now up to version 0.7.17, 0.7.12 was released in December of 2014. The solution is to upgrade your BWA version ...
written 7 weeks ago by Dan Gaston7.1k
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Comment: C: Checking kinship coefficients and relationships and comparing genotyping data to
... I would assume it uses all of the SNPs in the genotype files you provide to it and not a selected subset or panel. ...
written 6 months ago by Dan Gaston7.1k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... I got you, well explained. That makes perfect sense. And the explanation is useful to the OP and other's reading this. ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... If I am doing a full alignment against a transcriptome, multi-mapping gives me information that I can use. I can still run that process and then get my counts at the gene level from a program like featureCounts, which I can give specific parameters to on how to handle multi-mapping reads. That was m ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... I work on humans and even there I do my gene-level and transcript-level analyses mostly independently from one another. We have extremely rapid count estimators and programs for dealing with these so it never makes sense to me to save a bit of time with a shortcut that introduces some additional wri ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... Unless the method you used only assigns a read count to a single transcript this really isn't a good way to do it. You are better off doing the counts at the gene level in the first place. ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Differential gene expression from RNAseq data. Before or after annotation?
... Do your counting at the gene level instead of the transcript level. If you are going the alignment route with say HiSat you just need to take the BAMs along with a gene annotation file and run featureCounts, then import that into DESeq2 for the estimation and differential expression analysis, no nee ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Indel concordance from different VCF files
... I think as long as your rules are reasonable it will be ok. A percent overlap works. You could also do something to merge close together indels that fall within a larger one. For instance, if program A calls a large indel of 100 bp and program B called two different 30bp indels close together you mi ...
written 9 months ago by Dan Gaston7.1k
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Comment: C: Explanation of a Perl script
... And the other thing the OP will need to know is the structure and contents of a FastQ file ([Description here][1]). [1]: https://en.wikipedia.org/wiki/FASTQ_format ...
written 9 months ago by Dan Gaston7.1k
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Answer: A: Indel concordance from different VCF files
... You basically need to define what rules you'll use for InDels being concordant. Usually, you'll go with some sort of overlap criteria. You'll also want to be sure you left-normalize all of the input VCFs. But from there, any sort of tools, like BEDTools that looks for intersections between genomic c ...
written 9 months ago by Dan Gaston7.1k

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Popular Question 23 days ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Popular Question 3 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Popular Question 8 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
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Scholar 15 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 17 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Great Question 17 months ago, created a question with more than 5,000 views. For Checking kinship coefficients and relationships and comparing genotyping data to exomes
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Scholar 18 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 20 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
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Popular Question 24 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Use Conservation Or Evolutionary Rate To Infer Functional Relevance Of Aminoacid
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Collapse Clades In A Newick Tree With Average Distance To Tips < X
Scholar 2.3 years ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 2.3 years ago, created an answer that has been accepted. For A: sequence alignment using a core alignment

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