User: d-cameron

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d-cameron2.0k
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Posts by d-cameron

<prev • 229 results • page 1 of 23 • next >
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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 days ago by d-cameron2.0k
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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 days ago by d-cameron2.0k
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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 6 weeks ago by d-cameron2.0k
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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 7 weeks ago by d-cameron2.0k
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Answer: A: Why call variant generate homozygous site with genotype 0/0, why it be reporte
... Reporting homozygous reference is important as it distinguishes that position from a no call position. To answer the question: do samples A and B have the same alleles at position X, you need to know what the alleles are in both samples. If your SNV caller is unable to call position X in one of the ...
written 9 weeks ago by d-cameron2.0k
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Answer: A: identifying transgene insertion site in WGS
... I've had success using [GRIDSS][1] to do this. I even included an example of doing this in the [GRIDSS paper][2]. In short you: - Add transgene to your mm10 reference - (optional depending on transgene sequence) mask (replace with Ns) the mouse homolog of your gene of interest - Align reads to mm1 ...
written 9 weeks ago by d-cameron2.0k
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Answer: A: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... > How do I parse the raw data of VCF in R? You already know the answer to that: it's the `readVcf()` function. You use the `VariantAnnotation` library to fully parse the file, or you use a text file parser if you need the raw input lines for some reason (you very rarely do). See [here][1] for ...
written 4 months ago by d-cameron2.0k
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Comment: C: Extract Hard-clipped and soft-clipped values from fifth column
... What is the larger problem that you are attempting to solve, and why only hard clips, not soft clips? Wouldn't it be easier to just use a utility such as `gridss.ComputeSamTags SOFTEN_HARD_CLIPS=true` to convert your hard clips into soft clips then do you conversion to BED? ...
written 6 months ago by d-cameron2.0k
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Comment: C: Help with .sam files _1,_2 from bowtie2 output into svDetect
... IF you really want to use bowtie2, The GRIDSS SV caller includes a gridss.SoftClipsToSplitReads utility program that will feed the soft clipped portion of the reads back to an aligner of your choice and convert them to split reads. Even works on the output of bwa which, somewhat surprisingly, result ...
written 6 months ago by d-cameron2.0k
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Comment: C: How to check breakpoint after detecting a CNV.
... Note that a CNV can be caused by more complex events that just simple duplication or deletions. For somatic SV in cancer, SVs are frequently caused my complex catastrophic rearrangements such as chromothripsis and chromoplexy. In such cases, paired flanking primers around the breakpoint are likely t ...
written 6 months ago by d-cameron2.0k

Latest awards to d-cameron

Scholar 6 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 4 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Supporter 6 months ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 13 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 14 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 14 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile 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: Please, please, define what a 'read' is.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 14 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 15 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

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