mm10 enhancer annotation for ngs.plot.r

Question

[m.sadman.sakib]

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!

[whm568019240]

Can ngs.plot build genome with local annotation file?

Answer 1

[BioinfGuru]

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