Search
Question: Plotting DataTrack for non-model organism.
0
gravatar for anupriyaverma1408
9 weeks ago by
anupriyaverma14080 wrote:

Hi all!

Today I was trying the package called 'Gviz' for plotting chip-seq peaks as histogram across the whole genome of Mycobacterium tuberculosis. But I was unsuccessful as it keep giving this error: 

Error in .normargGenome(value, seqnames(x)) : 
  supplied 'genome' must be a vector or factor

 These were the steps I was running:

library(Gviz)
library(GenomicRanges)
library(GenomicFeatures)

txdb <- makeTxDbFromGFF("/home/m.tub1.gff3",circ_seqs=character(), organism="Mycobacterium tuberculosis")
annoData <- genes(txdb)
annoData1 <- as.data.frame(annoData)
a <- annoData1[which(annoData1$end == max(annoData1$end)),]

a$label= "+"
a$label1= "-"


bed_file1 = read.csv("/home/peak_annotations_forward_strand.txt", header = T, sep = "\t")
bed_file2 = read.csv("/home/peak_annotations_reverse_strand.txt", header = T, sep = "\t") 

b <- bed_file1$pileup
c <- -(bed_file2$pileup)

gtrack <- GenomeAxisTrack(range = makeGRangesFromDataFrame(data.frame(seqnames=as.character(a$seqname), start=1, end=a$end)))


lim <- c(0, a$end)
dtrack <- DataTrack(data = c, start = bed_file1$start, end = bed_file1$end, name = "Peaks (+)")
dtrack1 <- DataTrack(data = d, start = bed_file2$start, end = bed_file2$end, name = "Peak (-)")

pdf(file="/home/trial_15sep.pdf",width=10,height=10)
plotTracks(list(dtrack, dtrack1), from = lim[1], to = lim[2], type = "histogram")
dev.off()


Can Gviz handle any non-model organism by taking FASTA or any other method ? Please help me out .

Thank you in advance.
 

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by anupriyaverma14080
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 136 users visited in the last hour