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User: d-cameron

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d-cameron • 2.1k
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Posts by d-cameron

<prev • 235 results • page 1 of 24 • next >
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Answer: A: Approach to structural variation analysis - case vs control
... 1,500 patients is an aweful lot of patients to have the same "rare" disease. Are these 1500 different rare diseases or all the one disease? The analysis I've seen done on rare diseases have used family trees of affected/not affected to prune the massive noise that you'll get by comparing population ...
written 6 days ago by d-cameron • 2.1k
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Answer: A: value of TLEN not conforming to the SAM specifications
... There are many, many SAM files where the content does not conform to the SAM specifications. In the case of TLEN, the TLEN definition was changed in a specification update but many tools (including GATK) were not updated to reflect this. The spec themselves have recently changed to acknowledge that ...
written 5 weeks ago by d-cameron • 2.1k
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Comment: C: Number of Tandem and Interspersed duplications
... Part of the problem is that many of the germline events are in regions that are difficult to call (microsattelite expansions are a good example of this). Have you considered using tools other than Delly? There have been a pair of benchmarking papers that came out recently https://genomebiology.bio ...
written 5 weeks ago by d-cameron • 2.1k
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Comment: C: Number of Tandem and Interspersed duplications
... If you don't care where they are inserted then you're actually asking a different question. What you want to be asking is how many copy number variants (do you only care about gain or loss as well?) there exist in a human genome. This information is readily available in database such as dgv (http:// ...
written 5 weeks ago by d-cameron • 2.1k
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Answer: A: Number of Tandem and Interspersed duplications
... At a high level, there are two classes of rearrangement detection. Those relying on copy number, and those relying on breakpoint detection. >Usually people refer to all interspersed duplications as "segmental duplcations" These are typically called by copy number callers. Such segmental duplica ...
written 6 weeks ago by d-cameron • 2.1k
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Comment: C: identifying transgene insertion site in WGS
... > Unfortunately we can't really identify the correct structure after the insertion. That does seem unusual. If you don't have any other compensating breakpoints, those calls indicate that the transgene is inserted on a double minute containing it and 7:28985942-36210528. The next steps I'd take ...
written 11 weeks ago by d-cameron • 2.1k
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Answer: A: BWA MEM Definition of a Primary Alignment
... The primary alignnent is not always the "left-most" on the query. This behaviour can be changed by supplying the "-5" flag in which case the alignment with the smallest coordinate will be reported as the primary. ...
written 4 months ago by d-cameron • 2.1k
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Comment: C: BWA MEM Definition of a Primary Alignment
... swbarnes2 answered your question regarding secondary alignments, but not supplementary alignments. > For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another posit ...
written 4 months ago by d-cameron • 2.1k
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Answer: A: how to output the best alignment rather than multiple alignments for each read i
... > did I miss something Reporting only the best alignment is the default in bwa mem (and bowtie2). By default, bwa reports some alternate alignments in the `XA` tag but you can ignore that. Note that for some reads the best alignment is chimeric so multiple alignment record will be reported for t ...
written 5 months ago by d-cameron • 2.1k
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Comment: C: identifying transgene insertion site in WGS
... Sorry for the delayed response. > Do you think I should try the new version (v. 2.2.0) again? I do. V2.0 added single breakend reporting which can be quite helpful in this sort of analysis. Whilst my collaborators supply an expected construct when engaging me, I've yet to have a project where ...
written 5 months ago by d-cameron • 2.1k

Latest awards to d-cameron

Scholar 6 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 4 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Scholar 5 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 8 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Popular Question 10 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 16 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 17 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 17 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 17 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 18 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 18 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 18 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
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