User: d-cameron
d-cameron • 2.2k
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Posts by d-cameron
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... 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 9 weeks ago by
d-cameron • 2.2k
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... 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 10 weeks ago by
d-cameron • 2.2k
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... > 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 12 weeks ago by
d-cameron • 2.2k
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... 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 12 weeks ago by
d-cameron • 2.2k
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... 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 12 weeks ago by
d-cameron • 2.2k
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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 12 weeks ago by
d-cameron • 2.2k
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... 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 12 weeks ago by
d-cameron • 2.2k
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... > 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 12 weeks ago by
d-cameron • 2.2k
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... What sex is your sample? ...
written 12 weeks ago by
d-cameron • 2.2k
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... [htsget][1] is the API for serving SAM/BAM/VCF over HTTP, but support is currently limited as it is a relatively new standard.
[1]: http://samtools.github.io/hts-specs/htsget.html ...
written 12 weeks ago by
d-cameron • 2.2k
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