## User: dustar1986

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8 months, 3 weeks ago
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#### Posts by dustar1986

<prev • 24 results • page 1 of 3 • next >
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... 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 9 months ago by dustar19860
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... 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 ...
written 9 months ago by dustar19860
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... Crystal clear like always. Thanks heaps Micheal! ...
written 12 months ago by dustar19860
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... 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 12 months ago by dustar19860
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... 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 12 months ago by dustar19860
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... 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 ...
written 12 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 21 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 21 months ago by dustar19860
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... 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 ...
written 21 months ago by dustar19860 • updated 21 months ago by florian.hahne@novartis.com1.6k
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... 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 2.0 years ago by dustar19860

#### Latest awards to dustar1986

Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 Design with Multiple Interactions

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