User: mario.keller.1988

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Posts by mario.keller.1988

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Gviz coverage and sashimi not from BAM file
... Hi, I was wondering if there is a way to plot coverage and sashimi plots without the need for a BAM file. This reason why I"m asking this is that I want to incorporate Gviz in a Shiny application on a server where I have limited space. I was wondering if it is somehow possible to provide the coverag ...
gviz written 4 weeks ago by mario.keller.19880
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Truncated Gviz plot
... Hi, I have a little aesthetic issue with my sashimi plots. ![enter image description here][1]. In all of my plots the sashimi numbers of the exon skipping event are cropped although there is enough space. Has someone experienced the same problem and knows a solution? I already changed all paramet ...
gviz sashimi plot written 10 months ago by mario.keller.19880 • updated 9 months ago by Robert Ivanek660
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Comment: A: DESeq2 for DE analysis in developmental stages of tomato pollen
... Thank you very much for your answers. What I still do not get is this part: Essentially, any truly global changes across stage is normalized away But I see between stage 3 and stage 1 around 10,400 downregulated, 4,250 upregulated and 1,350 not DE genes. Aren't this global changes and not normalize ...
written 2.4 years ago by mario.keller.19880
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Comment: A: DESeq2 for DE analysis in developmental stages of tomato pollen
... I'm not sure if I understand you correctly. Should I trust the DESeq2 results or not? The housekeeping gene I checked was never tested along the development of pollen so I am not sure if I can draw any conclusions from it. ...
written 2.4 years ago by mario.keller.19880
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DESeq2 for DE analysis in developmental stages of tomato pollen
... Hey guys, I have the following scenario. We performed MACE experiments (like RNA-seq but you produce only one read per transcript) for three developmental stages of tomato pollen (3 biological replicates for each stage). On the one hand I produced RPM values for all genes by normalizing simply for ...
normalization deseq2 de written 2.4 years ago by mario.keller.19880

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