Hi there, I'm trying to generate a locus plot with the ideogram, gene track from UCSC, along with SNPs and other featured track in the hg19 version of the human genome.

Code:

library(Gviz) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(GenomicInteractions) library(rtracklayer)

from <- 61547834 to <- 61565833

knownGenes <- UcscTrack(genome = "hg19", chromosome = "chr11", track = "knownGene", from = from, to = to, trackType = "GeneRegionTrack",rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name2", transcript = "name", strand = "strand",fill = "#960000", name = "Genes")

txdb_hg19 <- TxDb.Hsapiens.UCSC.hg19.knownGene

txTranscriptsv1 <- GeneRegionTrack(txdbhg19, genome="hg19", chromosome="chr11", showId=TRUE, geneSymbol=TRUE, name="UCSC")

library(org.Hs.eg.db)

symbols <- unlist(mapIds(org.Hs.eg.db, gene(txTranscripts_v1), "SYMBOL", "ENTREZID", multiVals = "first"))

symbol(txTranscriptsv1) <- symbols[gene(txTranscriptsv1)]

snpLocations <- UcscTrack(genome = "hg19", chromosome = "chr11", track = "snp151", from = from, to = to, trackType = "AnnotationTrack", start = "chromStart", end = "chromEnd", id = "name",feature = "func", strand = "strand", shape = "line",stacking = "dense", fill = "black", name = "SNPs")

enh <- UcscTrack(genome = "hg19", chromosome = "chr11", track = "vistaEnhancers", from = from, to = to, trackType = "AnnotationTrack", start = "chromStart", end = "chromEnd", id = "name",feature = "func", strand = "strand", shape = "line", fill = "black", name = "Enhancer")

plotTracks(list(ideogram.track, genome.axis.track, txTranscripts_v1, snpLocations, enh), from = from, to = to, showTitle = TRUE)

But when I look at the plot, I don't see any SNPs or Enhancers marked in the region. What am I doing wrong?

Hi,

There were several issues in your code, you need to pay attention to extract correct information from UCSC tables. You also did not provide code which works. There were some parts missing and few typos. Here is the code which works for me.

Best Robert

library(rtracklayer)
library(Gviz)
library(GenomicInteractions)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)


from <- 61310001
to <- from+2e4-1

ideogram.track <- IdeogramTrack(chromosome="chr11", genome="hg19")

genome.axis.track <- GenomeAxisTrack()

txTranscripts_v1 <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg19.knownGene, genome="hg19", chromosome="chr11", showId=TRUE, geneSymbol=TRUE, name="UCSC")
symbols <- unlist(mapIds(org.Hs.eg.db, gene(txTranscripts_v1), "SYMBOL", "ENTREZID", multiVals = "first"))
symbol(txTranscripts_v1) <- symbols[gene(txTranscripts_v1)]

snpLocations <- UcscTrack(genome = "hg19", chromosome = "chr11", track = "snp151Common", from = from, to = to, trackType = "AnnotationTrack", start = "chromStart", end = "chromEnd", id = "name",feature = "func", strand = "strand", shape = "box", stacking = "dense", fill = "black", name = "SNPs")

enh <- UcscTrack(genome = "hg19", chromosome = "chr11", track = "vistaEnhancers", table="vistaEnhancers", from = from, to = to, trackType = "AnnotationTrack", start = "chromStart", end = "chromEnd", id = "name", shape = "box", fill = "black", name = "Enhancer")


plotTracks(list(ideogram.track, genome.axis.track, txTranscripts_v1, snpLocations, enh), from = from, to = to, showTitle = TRUE)