annotatePeaks.pl without annotation in genes name

Question

[xiaoxiazhong053]

Hi, guys, i am using homer to do analysis of chip-seq data, however, and when I used annotate.pl to do the annotation of my peak calling.txt, I found that there is no any annotation in gene name or some other column which are important for me, so would you like to help me to figure this out? I really tried a lot to get it, but it still does not work.

[Sej Modha]

Can you post the command that you have used to annotate the peaks?

[ATpoint]

Please post a few lines of your input file and the command line.

[Arup Ghosh]

Please share the command you have used.

Answer 1

[Prakash]

In Homer, there is annotatePeaks.pl which annotates the peak to nearest gene