User: d-cameron

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d-cameron2.2k
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Posts by d-cameron

<prev • 263 results • page 2 of 27 • next >
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Answer: A: HPV EBV typing from cancer genome data
... The fastest way to type the viruses directly from the fastq data would be to use a kmer abundance tool such as kraken2. This approach is fast as it performs neither alignment nor assembly. If you want to know the actual sequence of the virus(es) in the sample, then you'll need to do assembly. ...
written 6 weeks ago by d-cameron2.2k
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Comment: C: how to output the best alignment rather than multiple alignments for each read i
... Yes. XA indicates an alternative alignment location. Read with XA indicate there could be other equally/almost as good alignment locations for this read. SA indicates that this alignment is part of a chimeric alignment (aka split read alignment). Reads with SA imply the read spans a structural var ...
written 4 months ago by d-cameron2.2k
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Comment: C: Why Samtools view don't extract sequence out of the given region?
... samtools *is* already returning the reads with alignments overlapping your region of interest. If a read is 100bp long and starts at position 1 with a perfect alignment, then it aligns to bases: [1-100] inclusive. If you ask for reads that overlap positions 100-200, samtools is going to return the ...
written 5 months ago by d-cameron2.2k
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Answer: A: Is structure variations detected in DNA panel sequencing should also be detected
... > So, My question is structure variations detected in DNA sequencing results should also exist in whole transcriptome sequencing results? The breakpoint? No. The vast majority of SVs occur outside of exonic sequence so the breakpoints will not be detected in RNA-seq data. Gene fusions are almost ...
written 5 months ago by d-cameron2.2k
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Answer: A: The center in scatter plot generated by CNVkit looks off
... This appears to be a sex determination issue. As per the CNVkit documentation: ``` By default, copy number calls and log2 ratios will be relative to a diploid X chromosome and haploid Y. ``` This can be adjusted if you know the sex of your sample (or you want CNVkit to predict for you). See https: ...
written 5 months ago by d-cameron2.2k
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Comment: C: The center in scatter plot generated by CNVkit looks off
... Do these other papers completely ignore Y for female sample? I know many pipeline just throw out anything on Y once the sample has been determined to be female. More sophisticated pipelines have extra logic to handle less common scenarios such as Downs and Klinefelter syndromes as, if you have a lar ...
written 5 months ago by d-cameron2.2k
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Answer: A: [IGV] Is it an aneuploidy ?
... The read pair you can posted looks completely normal for 2x151bp sequencing of a 270bp long DNA fragment. > Is it an aneuploidy ? Aneuploidy requires more than just a single read. > The F2R1 can also change to F1R2 All at indicates is which strand the fragment was sequenced from. >It ...
written 5 months ago by d-cameron2.2k
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Comment: C: The center in scatter plot generated by CNVkit looks off
... So why are you worried about the CN profile on the Y chromosome? There is no Y in your samples so everything you're seeing can be explained being one of the pseudoautosomal regions, or has homology with an autosome. ...
written 5 months ago by d-cameron2.2k
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Answer: A: Split bam into chunks but keep reads mapped to the same region together
... > I need to split enormous bam files into smaller pieces, to parallelize haplotype calling Indexed BAM supports random access so there no technical reason why you have to split the bam at all. Many good callers will be able to multi-thread the calling. Other callers will have a parameter to spec ...
written 5 months ago by d-cameron2.2k
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Comment: C: The center in scatter plot generated by CNVkit looks off
... What sex is your sample? ...
written 5 months ago by d-cameron2.2k

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Scholar 21 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
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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Popular Question 15 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
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Popular Question 19 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: Modernising the FASTQ Format
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 19 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: Modernising the FASTQ Format
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 21 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
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Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.4 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.4 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.4 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.4 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

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