User: i.sudbery
i.sudbery • 1.3k
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- IanSudbery
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- 5 days, 5 hours ago
- Joined:
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- Email:
- i********@sheffield.ac.uk
Posts by i.sudbery
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... To answer your actaul question... Its like this because this is what is actually stored in a BAM file, which are not quite just compressed SAM files. pysam acts as a wrapper around the htslib c library, which is the same thing samtools uses, and that returns a c-structure representing the read rathe ...
written 5 weeks ago by
i.sudbery • 1.3k
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... In order to print an AlignedSegment out as a formatted SAM entry you need to use the `tostring` method and supply the AlignmentFile that the AlignedSegment came from. This contains the mapping of the numeric contig ids to the string contig names and also the encoding for the quality scores.
Thus yo ...
written 5 weeks ago by
i.sudbery • 1.3k
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... A very exciting 4-year PhD opportunity has arisen for a capable student to work in the Wilson/Sudbery labs at the University of Sheffield together with a **world leading biologics R&D company** on a project encompassing **synthetic biology, gene expression and computational biology**. Students ...
written 7 weeks ago by
i.sudbery • 1.3k
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... Do you have a reference for an enhancer that has been definitely demonstrated to act by a mechanism other than co-localisation with the promoter? I'd love to read that. ...
written 9 weeks ago by
i.sudbery • 1.3k
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... Gold standard for enhancers would be to clone into a reporter vector, show expression of reporter in an identical pattern to the wildtype candidate target, show that cloned fragment is the minimal piece that exhibits this pattern and show that this activity is independent of distance from, and orien ...
written 9 weeks ago by
i.sudbery • 1.3k
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... Basically, the answer is that you can't. You can't really assign enhancers to genes without C data and expression data. You can probably make some educated guesses with one or the other of those data sets, particularly if you have two conditions, but without either, you are pretty stuck.
Probably ...
written 9 weeks ago by
i.sudbery • 1.3k
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... Yes, its wrong to just blindly annotate enhancers to their nearest gene. The number of enhancers that regulate their nearest gene varies from study to study. The number I have in my head is 65% of enhancers do not regulate the closest gene (although I can't right now find the reference). There is so ...
written 9 weeks ago by
i.sudbery • 1.3k
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... (A - (B+C)/2) - (B-C) = (20 - (30+10)/2) - (30-10) = (20-20) -20 = -20
So yes, it would be significant, BUT what that would be telling you is that the gene is significantly less up in condition than other conditions, where as a positive value would be telling up it was more up. ...
written 9 weeks ago by
i.sudbery • 1.3k
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... How about an (A-(B+C)/2) - (B-C) model? ...
written 9 weeks ago by
i.sudbery • 1.3k
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... How about trying to building your linear model to do a difference of differences test? You want to ask if the difference between the A/notA samples is bigger than the B-C difference.
I suspect Gordon Smyth is the person to ask hope to do this, although you might need to be happy using limma voom/ed ...
written 9 weeks ago by
i.sudbery • 1.3k
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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