Hi,

I am trying to do TE expression analysis, while for the TE annotation gtf file, the file download from the http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/, for the 3rd column of the rmsk gtf file GRCh38_GENCODE_rmsk_TE.gtf, the features are all exon, so it seems the annotation file are all in the coding region.

Is there an "whole length TE annotation file", which including both the exon, intron, and maybe other genomic regions.

Thank you so much for any instructions.

Best,