Question: IGV like plots with GViz
gravatar for Deepak Tanwar
11 months ago by
McGill University, Canada
Deepak Tanwar10 wrote:

Hello everyone,

I would like to create coverage plots like IGV (like we obtain after autoscale)

How I am trying to do?

  1. Read the bam files with windowCounts from csaw package`.
  2. Normalized the read counts.
  3. code to make data track:
track <- DataTrack(range = data,
                       genome = gen,
                       type = "histogram",
                       name = "normalized track",
                       window = -1,
                       chromosome = chr,
                       color = col,
                       fill=col, col.histogram=col,
                       background.title = rcol,
                       trackType = "DataTrack")

Plots I a getting are not same as they are displayed on IGV

How can I improve my coverage plot?

ADD COMMENTlink modified 11 months ago • written 11 months ago by Deepak Tanwar10
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