User: i.sudbery

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i.sudbery1.3k
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IanSudbery
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Posts by i.sudbery

<prev • 132 results • page 1 of 14 • next >
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Comment: C: Pysam changes bam format when printing
... 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.sudbery1.3k
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Answer: A: Pysam changes bam format when printing
... 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.sudbery1.3k
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Job: PhD: Exciting wet/dry synthetic biology PhD opportunity with industrial links at the University of Sheffield
... 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 ...
phd job written 7 weeks ago by i.sudbery1.3k
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... 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.sudbery1.3k
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... 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.sudbery1.3k
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... 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.sudbery1.3k
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Answer: A: Is annotation of enhancers to nearest gene pointless?
... 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.sudbery1.3k
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Comment: C: DESeq2: Find differentially expressed genes specific to one condition
... (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.sudbery1.3k
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Comment: C: DESeq2: Find differentially expressed genes specific to one condition
... How about an (A-(B+C)/2) - (B-C) model? ...
written 9 weeks ago by i.sudbery1.3k
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Comment: C: DESeq2: Find differentially expressed genes specific to one condition
... 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.sudbery1.3k

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Scholar 5 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Scholar 3 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Popular Question 4 months ago, created a question with more than 1,000 views. For StringTie: To use a reference gene-set or not?
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Scholar 9 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Scholar 11 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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