User: i.sudbery

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

<prev • 129 results • page 1 of 13 • next >
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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 7 days 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 7 days 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 7 days 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 7 days 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 10 days 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 11 days 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 12 days ago by i.sudbery1.3k
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Answer: A: Public datasets with UMI
... Try the datasets referenced in this paper: https://www.ncbi.nlm.nih.gov/pubmed/28100584 ...
written 13 days ago by i.sudbery1.3k
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Comment: C: high duplicated level in SRA
... Fastqc is also only single-ended duplication levels. Its not possible to measure duplication levels pre-alignment. At best a program might test for the identity of the sequence in both end of a pair. But reads can be duplicates without having identical sequences (e.g. via sequencing errors). The o ...
written 14 days ago by i.sudbery1.3k
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Comment: C: Does allele refer to the entire gene sequence or one position of the gene sequen
... I agree. Sort of. For example, the term that I don't really think makes sense these days in animal genetics is "gene". The complex nature of our modern understanding of inheritance means that genes are originally defined don't exist. There are things we reffer to as genes today, but they aren't t ...
written 22 days ago by i.sudbery1.3k

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