Question: mm10 enhancer annotation for ngs.plot.r
gravatar for sikhtechai
2.5 years ago by
sikhtechai30 wrote:

Hi! I have used ngs.plot for plotting ChIP-seq reads over promoter or genebodies. But I was interested to see the peak profile over enhancers. My reads are mapped to mm10 and for that, ngsplot doesn't have enhancer annotation. One solution I thought would be to remap on mm9 and reanalyze. Or, maybe use "liftover" tool in UCSC to covert mm9 enhancer bed file to mm10. In that way, one might lose some information, but I will keep it as a last resort.

So, does anyone have a workaround on how to use ngs.plot to visualize enahancer for mm10 mapped ChIP- seq reads?

Many thanks in advance!

visualization chip-seq peak • 1.5k views
ADD COMMENTlink modified 14 months ago by whm5680192400 • written 2.5 years ago by sikhtechai30

Can ngs.plot build genome with local annotation file?

ADD REPLYlink written 14 months ago by whm5680192400
gravatar for YaGalbi
2.4 years ago by
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

Why are you not just using the UCSC genome browser with a custom track? remapping to another build is not ideal

ADD COMMENTlink written 2.4 years ago by YaGalbi1.4k
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