Calculating percentage TEs content (%) for a genome

Question

[lukhanyomakhabane]

Dear all How can one calculate percentage transposable content for a genome (% TE content). For example, I have Identified a total of 5137877 TEs for a genome assembly of size 32614401 bp. However, I want to express TE as percentage (%). So how I do that? Your help would be greatly appreciated.

Answer 1

[Buffo]

TE as a percentage of the total genome would be the total length of the genomic sequence that is annotated as TEs. Be careful, repeat content is not the same as TEs, neither the total length of genes annotated as TEs. Full-length TEs may include coding and non-coding sequences.