Where 02_Ltr_and_classfier.pl

[GooLey1025]

Hello, thanks for sharing your code . I am very amazed by your work !
And I want to know where is this perl file .

/path/to/your/local/RepeatModeler-master/02_Ltr_and_classfier.pl

In my RepeatModeler software directory , I do not find this 02_Ltr_and_classfier.pl .
I would appreciate it for your any reply .

[GooLey1025]

Add sth : this code is in
Rice-pan-genome-analysis/01Pan_Ltr_database_build/02_Ltr_class.pbs

source activate /public/home/huangyj/anaconda3/envs/repeatscout
##job area
##Step1
perl /public/home/huangyj/software/RepeatModeler-master/02_Ltr_and_classfier.pl -threads 5 -database $speciesname -LTRStruct

[Ne0tea]

Sorry for the late reply. 02_Ltr_and_classfier.pl is a part of script from repeatmodeler pipeline and took out for always encounterring errors without throwing the error properly to run seoarately.
I have added it in Rice-pan-genome-analysis/01Pan_Ltr_database_build and let me know if there are any more questions.

[yaoxkkkkk]

Hi thank you for your sharing, I wonder whats the meaning of "encountering errors without throwing the error"? Will this pipeline improve the annotation quality of LTR?

[yaoxkkkkk]

Sorry for interupting again. If the LTR Structural Analysis step has already been successfully executed within the RepeatModeler pipeline, is it necessary to run the 02_Ltr_and_classifier.pl script separately? Would skipping this step have any impact on downstream analyses or the quality of the LTR annotations?

[GooLey1025]

For this process， I do not have any deep understanding， but I turned to EDTA， which can do de novo LTR annotation using repeatmodeler also.