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Question: Rice genome ideogram construction
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gravatar for sabrina.elias
11 months ago by
sabrina.elias0 wrote:

Hi All

I was having difficulty in constructing an ideogram for rice genome using gviz, since in UCSC rice genome is not included. I also wanted to export annotation information for specific regions. As gviz provide a nice view for this presentation i was trying to use it, but could not do it properly. 

Florian helped me by modifying my codes as below.

Posting it here thinking it might be helpful for someone else also. 

I was having difficulty with gieStain option also. If anyone can help with that.

 

thanks

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library(ggbio)

library(Gviz)

library(BSgenome.Osativa.MSU.MSU7)

idTable <- data.frame(chrom=tolower(seqnames(BSgenome.Osativa.MSU.MSU7)), chromStart=0, chromEnd=seqlengths(BSgenome.Osativa.MSU.MSU7),name=seqnames(BSgenome.Osativa.MSU.MSU7), gieStain="gneg", stringsAsFactors=FALSE)

idTrack <- IdeogramTrack(bands=idTable, genome="MSU7")

library(biomaRt)

mart = useEnsembl(biomart="plants_mart", host="plants.ensembl.org", dataset = "osativa_eg_gene")

bm <- useMart(host = "plants.ensembl.org", biomart="plants_mart", dataset = "osativa_eg_gene")

fm <- Gviz:::.getBMFeatureMap()

fm["cdsl"] <- c("cds_start", "cds_length")

fm["symbol"] <- c("external_gene_id", "external_gene_name")

biomTrack <- BiomartGeneRegionTrack(chromosome = 1, start = 20000000, end = 21000000, biomart=bm, featureMap=fm)

plotTracks(list(idTrack, biomTrack), transcriptAnnotation="symbol")

 

ADD COMMENTlink written 11 months ago by sabrina.elias0
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