User: d-cameron

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d-cameron1.1k
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Posts by d-cameron

<prev • 127 results • page 1 of 13 • next >
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Comment: C: annotation of SV (structural variants)
... Reciprocal translocations should have two separate translocation events at the same position. Depending on the DNA repair mechanism, the 'same' position are usually slightly different positions. ...
written 3 days ago by d-cameron1.1k
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Comment: C: annotation of SV (structural variants)
... The special case handling for DELLY TRA code can be found https://github.com/PapenfussLab/StructuralVariantAnnotation/blob/master/R/extensions-VCF.R#L336 . I just reviewed the code and the custom DELLY 5to5 and 3to3 attributes are not used for inversions (I just found this issue myself with manta I ...
written 4 days ago by d-cameron1.1k
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Comment: C: annotation of SV (structural variants)
... In my gene fusion example code, gene orientation and the breakpoint direction must be consistent with the fusion. An upstream gene in the fusion must have the strand matching the breakpoint orientation (`+` strand transcript would require a `+` breakpoint orientation), and the downstream gene requir ...
written 4 days ago by d-cameron1.1k
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Comment: C: annotation of SV (structural variants)
... StructuralVariantAnnotation will convert the output of SV callers into the same GRanges format regardless of whether the caller used TRA/BND or DEL/DUP/INV format to make the call. It works with VCFv4.2 or VCFv4.3 compliant output, but I've added some extra code to handle some of the more popular ca ...
written 8 days ago by d-cameron1.1k
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Comment: C: annotation of SV (structural variants)
... + indicates that the DNA before the breakpoint is involved in the adjacency, - is the other orientation. For a 500bp chr1 the following GRanges chr1 100 + chr1 200 - Would indicate a deletion as the DNA leading up to chr1:100 is connected to the DNA at chr1:200 and beyond. ...
written 8 days ago by d-cameron1.1k
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Comment: C: annotation of SV (structural variants)
... > please would it be possible to share a piece of R code that uses "findBreakpointOverlaps(gr)" in order to infer the overlap of the breakpoints with exons, introns or intergenic regions ? The nice thing about the breakpoint format I'm using (a normal bioconductor GRanges object with just an ext ...
written 17 days ago by d-cameron1.1k
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Comment: C: Research Consultation for a phD Dissertation
... > Now I'm a phD student intending to complete my research path on the same field, but I have a problem starting from that point because the original idea is owned by my former supervisors and I'm not allowed to proceed with it. Clearly there is more going on that outlined. Research ideas are not ...
written 25 days ago by d-cameron1.1k
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Comment: C: What kind of sequences I have, haploid or diploid?
... Just a point on terminology: SNV: single-nucleotide variant SV: structural variant These are very different variant types. ...
written 25 days ago by d-cameron1.1k
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Answer: A: annotation of SV (structural variants)
... This very much depends on what sort of annotation you want to do. If you're interested in breakend overlap annotation, then I recommend using my StructuralVariantAnnotation package to convert to a paired breakend GRanges object then using the standard bioconductor packages to annotate stuff like re ...
written 25 days ago by d-cameron1.1k
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Comment: C: Fragment size and insert size
... If you're interested in STRs, you should not merge paired end reads as the merge will (almost always) be incorrect when the inner portion of the fragment contains a short tandem repeat motif. ...
written 9 weeks ago by d-cameron1.1k

Latest awards to d-cameron

Guru 10 weeks ago, received more than 100 upvotes.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Centurion 3 months ago, created 100 posts.
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 5 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 9 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 9 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 11 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 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: Please, please, define what a 'read' is.

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