User: Ron
Ron • 970
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... Hi,
I am trying to visualize gene fusions from RNAseq data in IGV, that is detected by gene fusion software STAR-fusion and Fusion catcher.
Does anybody know of steps to do this?
I always find it complex to how to color,sort, group the reads so as to visualize the gene fusion.
This post is informa ...
written 4 months ago by
Ron • 970
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... STAR + featurecount/htseq-count is a very good pipeline to use. ...
written 5 months ago by
Ron • 970
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... Also EBseq.
http://bioconductor.org/packages/release/bioc/html/EBSeq.html
It provides different possible patterns between multiple conditions. ...
written 5 months ago by
Ron • 970
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Comment:
C: Drugs targeting Gene Fusions
... So it is best to look at drug interactions with the gene fusion themselves ? I mean , A drug that would work for lets say ERBB2--CDK12 fusion would not work for ERBB2--PGAP3 fusion ? Or it can be considered druggable , based on how the gene fusion product is ?
On the contrary, it seems NTRK fusion ...
written 6 months ago by
Ron • 970
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... Hello ,
I wanted to know if gene fusions from RNAseq data can be said druggable based on one of the genes being druggable or it has to be druggable as a fusion ?
I would like to look into the drugs that bind to the genes from fusions,so which one would be the right way to look into the data.
This ...
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... hello @Malachi Does this database (http://dgidb.org/downloads ) includes information from the resources listed above? or could you provide info on how it was created ? I read this page and http://dgidb.org/getting_started "drug-gene interactions have been mined from DrugBank, therapeutic target da ...
written 6 months ago by
Ron • 970
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... I posted the link to the data and the paper. ...
written 6 months ago by
Ron • 970
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... Hi all,
Does somebody know which package can be used for plots like this?
> The dot plots illustrates the number of detected fusion transcripts per megabase per sample normalized by the sequencing coverage. Tumor types were sorted according to the fraction of samples with fusions.
I am tryi ...
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... For extracting the clusters based on Columns.(ComplexHeatmaps)
mat = matrix(rnorm(80, 2), 8, 10)
mat = rbind(mat, matrix(rnorm(40,-2), 4, 10))
rownames(mat) = letters[1:12]
colnames(mat) = letters[1:10]
HM <- Heatmap(mat, km=3 , column_km = 3) HM
for (i in 1:len ...
written 7 months ago by
Ron • 970
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... A follow up question - I also want to count the percentage of UTR's ,exons in my bed file ,so the way would be downloading a bed file for both of them separately(UTR's ,exons) and doing the intersect with the complete bed file of interest? ...
written 8 months ago by
Ron • 970
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