search

mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
206 stars 29 forks source link

library requirement for tetoolkit #28

Closed zy041225 closed 6 years ago

zy041225 commented 6 years ago

Hi,

I plan to use tetoolkit to estimate TE expression in some species. However, I wonder if there's requirement in library construction step. Specifically, if the library I used is polyA-selected, would it cause some bias when estimate TEs' expression?

Best, Yang

olivertam commented 6 years ago

Hi Yang,

There is a recent publication on TCAG samples that suggest that polyA-selected libraries might not show the full profile of TE expression. Thus, it might be better to generate libraries from total RNA, rather than polyA-selected RNA. Thanks.

Cheers, Oliver

zy041225 commented 6 years ago

Hi Oliver,

Thanks for confirming my guess. I'll try to find some RNA-seq data that are from total RNA.

Best, Yang