Create library of TEs de novo

Question

[kirillkirilenko]

I have 8 chromosomes assemblies of different species belonging to the same genus (Anopheles) and I want to compare these assemblies by percentage of repetitive DNA, TEs distribution etc. As far as I know there is no curated library of TEs for Anopheles species and I decided to create my own library. I used both RepeatModeler and EDTA (https://github.com/oushujun/EDTA that seems to me the better choice). Here is the question: Should I construct a library for all species (e.g. combine all .fasta files) and then annotate genomes using this single library or I should create 8 different libraries for all species? Thank you in advance!

Answer 1

[lieven.sterck]

Personally I would make big single library.

it is very well possible that in a genome you find a good copy of a TE to be added to the library that in most other genomes is not so good. Since you have a good rep from a genome you can use that to screen the other genomes as well (especially since they are from same genus).

It will be afterwards also easier to compare the results I assume, if you only use an overall merged TE library