The use of EDTA_raw.pl and EDTA.pl

[qdu-beep]

I would like to ask if I want to obtain the genome sequence with only LTR regions masked and using soft-masking, should I follow the steps below? The main question is whether I should use EDTA.pl after using raw_EDTA.pl. I would greatly appreciate your response!

Should I use EDTA_raw.pl with the -type ltr to obtain the raw library of LTR?
And then, should I use EDTA.pl with the --overwrite 0 to further annotate and filter based on the results of raw_EDTA.pl?
Finally, I should use make_masked.pl for soft masking.

I came across the following description on the website, but I'm not sure if my understanding is correct. Thank you for your assistance!
"Users may run EDTA_raw.pl for each TE type with --threads 1, then run EDTA.pl with multi threads and --overwrite 0"(https://github.com/oushujun/EDTA/releases)
Originally posted by @qdu-beep in #61 (comment)

[oushujun]

Hello,

If you are only interested in the LTRs, you should just run LTR_retriever. The EDTA_raw.pl --type ltr will get you there, but without whole-genome annotation. You can do your own by running RepeatMasker -lib $genome.mod.LTRlib.fa within EDTA.raw/LTR/. After RepeatMasking, you can run make_masked.pl for soft masking.

Shujun

[qdu-beep]

Hello,

If you are only interested in the LTRs, you should just run LTR_retriever. The EDTA_raw.pl --type ltr will get you there, but without whole-genome annotation. You can do your own by running RepeatMasker -lib $genome.mod.LTRlib.fa within EDTA.raw/LTR/. After RepeatMasking, you can run make_masked.pl for soft masking.

Shujun

Dear oushujun,

Many thanks for your useful reply! My question has been resolved!

Sincerely,
qdu-beep