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Question: about UCSCtrack in Gviz
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gravatar for Bogdan
2.4 years ago by
Bogdan490
Palo Alto, CA, USA
Bogdan490 wrote:

Dear Florian, and all,

I am running the following code in Gviz in order to visualize the genes and the genetic variants :

ENSEMBL genes that are displayed with BiomartGeneRegionTrack are shown, but not the RefSeq or GENECODE genes; it would be very helpful if you could let me know how we can fix the display.

many thanks,

bogdan

 


library("Gviz")
library("biomaRt")
library("BSgenome.Hsapiens.UCSC.hg38")

transcript <- "ENST00000262189"

##

hg38 <- useMart("ensembl", "hsapiens_gene_ensembl")
transcript_ENSEMBL <- BiomartGeneRegionTrack(biomart = hg38, transcript = transcript)

### making a sequence track

sequence_track_ucsc <- SequenceTrack(Hsapiens)

 

start <- 152273760
end <- 152273780

 

ucscGene <- UcscTrack(genome="hg38", track="knownGene", trackType="GeneRegionTrack", chromosome="chr7")

refGene <- UcscTrack(genome="hg38", track="refGene", trackType="GeneRegionTrack", chromosome="chr7")

plotTracks(c(transcript_ENSEMBL, ucscGene, refGene,  sequence_track_ucsc), chromosome="chr7", from=start, to=end)

 

 

ADD COMMENTlink modified 2.4 years ago by Robert Ivanek530 • written 2.4 years ago by Bogdan490
1
gravatar for Robert Ivanek
2.4 years ago by
Robert Ivanek530
Switzerland
Robert Ivanek530 wrote:

You need to provide additional parameters for the UcscTrack function (exon starts and ends, transcript names)
 

ucscGene <- UcscTrack(genome="hg38", track="knownGene", trackType="GeneRegionTrack", chromosome="chr7", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name", transcript = "name", strand = "strand", from=start, to=end)

refGene <- UcscTrack(genome="hg38", track="refGene", trackType="GeneRegionTrack", chromosome="chr7", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name2", transcript = "name", strand = "strand", from=start, to=end)

 

 
ADD COMMENTlink written 2.4 years ago by Robert Ivanek530

thanks Robert !

ADD REPLYlink written 2.4 years ago by Bogdan490
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