User: d.depledge

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d.depledge • 0
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Posts by d.depledge

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Comment: C: GVIZ stacking error
... That works a treat! Thank you for your help on this. ...
written 11 weeks ago by d.depledge • 0
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Comment: C: GVIZ stacking error
... Did you have any joy with relaxing the parameters? Alternatively, do you know a way I can change the resolution in the plotting device to prevent this happening ? ...
written 3 months ago by d.depledge • 0
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Comment: C: GVIZ stacking error
... Wondering if anyone has a handle on this yet? it's a very curious issue... ...
written 3 months ago by d.depledge • 0
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Comment: C: GVIZ stacking error
... While the first problem is resolved - here is a second one using this simple GFF3 \##gff-version 3 \##sequence-region Ad5 1 35938 Ad5 RefSeq gene 4057 5836 . - . ID=gene.IVa2;Name=gene.IVa2 Ad5 RefSeq mRNA 4057 5836 . - . ID=mRNA.IVa2;Parent=gene.IVa2;Name=IVa2;class=late Ad5 RefSeq ...
written 3 months ago by d.depledge • 0
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Comment: C: GVIZ stacking error
... As it happens I have managed to solve the problem. The curiosity is that the error was solved simply by renaming a gene (and it's associated mRNA) from pics -> vex. Interestingly, I could replicate this error (or variations thereof) by changing any of my gene names to anything starting with 'pi. ...
written 3 months ago by d.depledge • 0
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GVIZ stacking error
... Hi, I'm using GVIZ with a custom built GFF3 file and am getting some curious artifacts in my output plot. The main issue is the false incorporation of an exon into a multi-exon unit (right side of image). Here the red hatched box shows the exon which should stand alone at the position indicated ...
gviz written 3 months ago by d.depledge • 0
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Comment: C: Differential Expression analysis between distinct scRNA-seq datasets
... Thanks for the comments - I've been looking at MAST and I think this might well suit my requirements.. Your point about cluster labels being data-driven is well taken and I will have to think carefully about interpretation. As for a confounded design, it is more the case of a poorly written descri ...
written 2.1 years ago by d.depledge • 0
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Differential Expression analysis between distinct scRNA-seq datasets
... I have two scRNA-seq datasets, both derived from a heterogeneous population of cells (comprising similar numbers of cell types and subpopulations). One sample has been treated with a drug, the other has not. While I can separate out the cellular subpopulations in each dataset, what I want is to then ...
differential gene expression scrna scrnaseq written 2.1 years ago by d.depledge • 0 • updated 2.1 years ago by davide risso • 830
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Gviz Alignments Track - RNASeq data
... I'm using GViz to visualize RNASeq data using AlignmentsTrack. I have lots of reads that are spliced across two or more exons (this is long read RNASeq data). However, I am getting an error when providing a character vector of CIGAR values associated with the alignment. "Error in .fillWithDefaults( ...
gviz written 3.2 years ago by d.depledge • 0

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