Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
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just • 0
@just-9837
Last seen 4.4 years ago

Hey guys,

I'm trying to load an annotation track from UCSC for H3K4me3 and H3Kme1 into gviz.

I used this

H3K4me3_H1ESC <- UcscTrack(track ="wgEncodeRegMarkH3k4me3", table = "wgEncodeBroadHistoneH1hescH3k4me3StdSig", trackType="AnnotationTrack",
                         genome='hg19', chromosome='chr1', from=from, to=to, feature="itemRgb",
                         stacking = "full")

Unfortunately, without a success.

I'd be really grateful for your help!

Any ideas what I can improve?

 

 

gviz ucsc • 846 views
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Robert Ivanek ▴ 680
@robert-ivanek-5892
Last seen 8 weeks ago
Switzerland

Hi Justina,

The table "wgEncodeBroadHistoneH1hescH3k4me3StdSig" contains signal (number of reads in 25 bp windows) for H3K4me3 mark and data is stored in bigwig file. Therefore you need to create a DataTrack object and not AnnotationTrack.

Here is an example:

library(Gviz)
chrom <- "chr1"
from <- 33003001
to <- 33008000
H3K4me3_H1ESC <- UcscTrack(track ="wgEncodeRegMarkH3k4me3",
                           table = "wgEncodeBroadHistoneH1hescH3k4me3StdSig",
                           genome="hg19", chromosome=chrom, from=from, to=to,
                           trackType = "DataTrack", name="H3K4me3 H1ESC",
                           start = "start", end = "end", data = "score",
                           type = "hist", window = "auto", col.histogram = "#08519C",
                           fill.histogram = "#08519C")
plotTracks(H3K4me3_H1ESC, from=from, to=to)

 

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