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!
•
written
by
m.sadman.sakib
1 answer
Why are you not just using the UCSC genome browser with a custom track? remapping to another build is not ideal
Log in to answer this question.
-
Tutorial: DNA Methylation: Sequencing Techniques
written by Novogene •
-
How to create a metagene profile plot
written by rebeccadistefano8 •
-
What kind of normalization to do when plotting aggragate plot using two different chip-seq bam files
written by baijiangshan9726 •
-
What could be the cause of different levels of binding in ChIP-Seq Input samples?
written by Aspire
-
Assigning nucleosome peaks to transcription factor bound locations(obtained by ChIP-seq)
written by sshibin •
-
R+Gviz: Fake AlignmentsTrack() to visualize Enhancer-Promoter connections
written by Matthias Zepper
-
Quantitative comparison of two different ChIP-seq data from same conditions
written by florian.noack •
-
[ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal profile plotting?
written by chiefcat
-
Removal of repeat and blacklist regions from ChIP-seq data
written by James Ashmore
-
Weird 1kb-periodic artifact in ChIP-Seq data (including input)
written by Ryan Thompson
Can ngs.plot build genome with local annotation file?