Moderator: Dan Gaston

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Dan Gaston7.0k
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Canada
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Last seen:
1 week ago
Joined:
6 years, 9 months ago
Email:
d************@deaddriftbio.com

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: 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 weeks ago by Dan Gaston7.0k
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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 weeks ago by Dan Gaston7.0k
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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 weeks ago by Dan Gaston7.0k
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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 10 weeks ago by Dan Gaston7.0k
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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 10 weeks ago by Dan Gaston7.0k
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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 11 weeks ago by Dan Gaston7.0k
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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 11 weeks ago by Dan Gaston7.0k
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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 11 weeks ago by Dan Gaston7.0k
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Answer: A: Meaning of 'tag' in the context of variants
... It is explained right in the text and answered by Jean-Karim above. The SNP that is being picked up as being associated with the phenotype is not causal but is in Linkage Disequilibrium with the true causal SNP. This is a pretty routine thing for GWAS analyses. ...
written 7 months ago by Dan Gaston7.0k
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Answer: A: calculate average target coverage from bam file
... While there are other tools to do the job, the issue is you appear to have 1) a mismatch between the installed version of samtools and where you are taking your appropriate command from and 2) your command line for specifying the input files is incorrect. The -a option is only found in the newer ver ...
written 7 months ago by Dan Gaston7.0k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Popular Question 5 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
Scholar 8 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 10 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Great Question 11 months ago, created a question with more than 5,000 views. For Checking kinship coefficients and relationships and comparing genotyping data to exomes
Teacher 11 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
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 11 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 14 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Teacher 14 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 17 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Use Conservation Or Evolutionary Rate To Infer Functional Relevance Of Aminoacid
Teacher 17 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
Popular Question 18 months ago, created a question with more than 1,000 views. For Bioinformatics Programmer and Analyst At Athletigen
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
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
Scholar 20 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Scholar 20 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment
Popular Question 20 months ago, created a question with more than 1,000 views. For Gatk'S Unifiedgenotyper And Genotype Determination
Scholar 21 months ago, created an answer that has been accepted. For A: sequence alignment using a core alignment

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