User: dustar1986

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dustar19860
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Posts by dustar1986

<prev • 24 results • page 1 of 3 • next >
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Answer: A: A bug when plotting Gviz data
... Hi Florian, Here is a link to my file. https://drive.google.com/file/d/0B0LC8cC9lS-yeUlBcS1TZjBkcW8/view?usp=sharing What I used to generate figure is new = read.table("Input.txt",header=T) newtrack <- GeneRegionTrack(new) gtrack <- GenomeAxisTrack() plotTracks(list(gtrack,newtrack),stack ...
written 10 weeks ago by dustar19860
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A bug when plotting Gviz data
... Hi, I found an interesting BUG in Gviz v1.20. I have a data frame `new` for transcripts, each line is an exon. Column names are `chromosome`, `start`, `end`, `width`, `strand`, `feature`, `gene`, `exon`, `transcript`, `symbol` and `color`. The information in `gene`, `transcript` and `symbol` are id ...
gviz written 10 weeks ago by dustar19860
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Comment: C: DESeq2 Dispersion Estimation after Applying Customized Normalization Factors
... Crystal clear like always. Thanks heaps Micheal! ...
written 5 months ago by dustar19860
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Comment: C: DESeq2 Dispersion Estimation after Applying Customized Normalization Factors
... Hi Michael. I was trying to simplify my question so I didn't make it clear. I'm doing exon inclusion rate comparison between conditions. The detail is: 1) my 'gc' matrix in the code records the number of spliced reads that connect an exon of interest to its two flanking exon neighbors. 2) then I c ...
written 5 months ago by dustar19860
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Comment: C: DESeq2 Dispersion Estimation after Applying Customized Normalization Factors
... Thanks Michael, I've added my code. I tried to re-start R session and re-run from the first line attached. It still gave me the same plot. ...
written 5 months ago by dustar19860
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DESeq2 Dispersion Estimation after Applying Customized Normalization Factors
... Hello,   I have counts from 32 RNA-seq samples and am trying to study drug effect using DESeq2. I have some trouble of understanding the dispersion estimation after applying a set of customized normalization factors.  First I used raw counts as input and called DESeq function directly. DESeq2 est ...
deseq2 written 5 months ago by dustar19860
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Comment: C: Gviz Color Filling
... Yes, I tried different parameters. Some of them are fixed but some ones never changed. I guess I'll do the remaining manually in Illustrator. Thank you so much for your help. It's a great visualization tool. ...
written 14 months ago by dustar19860
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Comment: C: Gviz Color Filling
... Thanks heap, Florian. It works perfectly, however it turned out a new question. I still have some exons not colored as expected. They were colored by the default yellow color which is not in my list. I found those exons are too close to their neighbors to be distinguished on the plot. Is that why th ...
written 14 months ago by dustar19860
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Gviz Color Filling
... Hi, I'm using Gviz to display transcripts. I wanna highlight some exons with different color. My input is a tab-separated plain text file like the following: new=read.table("myfile",header=T) head(new,1) chromosome  start  end width strand   feature   gene exon transcript color 1  chrX 586072 ...
gviz written 14 months ago by dustar19860 • updated 14 months ago by florian.hahne@novartis.com1.5k
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Comment: C: RUVSeq and Generalised Linear Mixed Model
... Thanks a lot for your comments Davide. That's really helpful. I also realised the noise from only using ERCC class B as negative control, as I'm down to 9 of them to pass the minimal reads threshold. I would try to re-estimate the unwanted effect using all the detected ERCCs across the samples (alth ...
written 17 months ago by dustar19860

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