User: d-cameron

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d-cameron2.1k
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Posts by d-cameron

<prev • 237 results • page 1 of 24 • next >
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Comment: C: bwa mem memory allocation, threads and nodes
... If a previous analysis was done, why aren't you using the bam files from that analysis? ...
written 18 days ago by d-cameron2.1k
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Answer: A: bwa mem memory allocation, threads and nodes
... Sequence alignment is an [embarrassingly parallel][1] computational task. That is, performance of bwa scales (almost) linearly with the number of threads provided. If you have a 24 core machine, you gain no benefit from running 3 8-thread bwa tasks in parallel instead of just running a single 24 th ...
written 18 days ago by d-cameron2.1k
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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 4 months ago by d-cameron2.1k
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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 months ago by d-cameron2.1k
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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 months ago by d-cameron2.1k
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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 months ago by d-cameron2.1k
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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 5 months ago by d-cameron2.1k
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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 6 months ago by d-cameron2.1k
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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 8 months ago by d-cameron2.1k
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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 8 months ago by d-cameron2.1k

Latest awards to d-cameron

Scholar 18 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 8 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Scholar 9 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 12 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Supporter 14 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 20 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 21 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 21 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 22 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 22 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 22 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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