I have some RNA-seq datasets from human cells and I am interested to see if the expression of transposable elements (TEs) change in different treatments. I found this easy to do with the plant Arabidopsis thaliana as the TAIR10 annotation of the genome has gene types that are TEs. However, such a gene type does not exist in for the human annotations I have seen https://www.gencodegenes.org/gencode_biotypes.html. My understanding is that repeats like TEs are masked in the released human genomes. Especially as so many TEs are so similar to each other, one could not assign RNA or DNA reads to a specific one, so you might need to look at it on the family level.
My question is, how can I get over this issue and look at RNA-seq data for TEs and all other transcript types in human cells? Are there any good studies that do look at expression changes in human cells that I can use to inspire an analysis approach?
There is a pipeline called RepEnrich . I myself want to test it but have not done so far. Articles citing this article are a good source for other similar pipelines/implementations
Thanks, that looks interesting. PDF downloaded!
This might help you... Please check this link...This is all about TE list ....Research review 2018.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753468/pdf/13100_2017_Article_107.pdf
Moved to comment. This is a review and does not answer the question of OP as t does not provide any technical help.