How to use HOMER with ensembl gtf and get detailed annotations

Question

[bencom]

Hello,

I’m super interested to use HOMER to annotate my RNAseq results. I would like to use Ensembl instead of RefSeq for consistency with other part of my project

I use the following command : annotatePeaks.pl Junctionpeaks.txt hg19 -gtf gencode_hg19.gtf > outputfile.txt

However in the output file I don’t have the repeated elements and the UTRs, while UTRs are present in my gtf

On the website it says : " The original HOMER annotation files are still used for the "Detailed Annotation" since the repeats will not be define in the GTF files.”

(http://homer.ucsd.edu/homer/ngs/annotation.html)

Has anyone encountered this problem before?

Thank you!