Investigating expression of potentially autonomous TEs identified.

Question

[lukhanyomakhabane]

Hello guys, I am planning to do expression of autonomous TEs families that I identified in genome of interest. This how I was planning to do it, I would like to ask if I am in the right pathway, any suggestion is welcomed. Thank you in advanced!

Sequences of TE families recovered will be aligned with pre-processed raw RNA-seq reads using Bowtie2. The expression levels of TEs will be quantified using RSEM, and normalized using Fragments Per Kilobase of transcript per Million mapped reads (FPKM) expression unit.