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oushujun
The percent of LINE is way below my expectation
Hi, @oushujun Thanks for developing EDTA. I am studying fall armyworm which is a lepidopteran pest. before using EDTA(1.9.8) to annotate assembly,i tried some methods to annotate this assembly.
- repeatmasker with repbase: SINEs: 0.61%, LINEs: 3.5%, LTR: 0.34%, DNA: 0.32%
- using repeatmodeler(2.0): SINEs: 0.89%, LINEs: 10.09%, LTR:1.91%,DNA: 1.54%, Unkown: 13.01% I used TEclass and ClassifyTE to classify Unkown consensus sequecne,most of consensus sequence was divided into DNA transposon.So i think percent of DNA transposon is much more than 1.54%
- using EDTA: SINEs: 0%, LINEs: 0.85%, LTR: 6.67%, DNA: 20.83% The change of DNA transposon is in my expections, but SINEs and LINEs is far from what I anticipated.
log.txt EDTA_Sf_1.e18701.txt GCF_011064685.1_ZJU_Sfru_1.0_genomic.fna.mod.tbl.txt
Hi, the SINE/LINE identification is carried out by RepeatModeler integrated in EDTA. If you have curated SINE/LINE sequences you may want to provide them to EDTA with the --curated parameter.
Shujun
On Mon, Jun 14, 2021 at 12:37 AM BonesAQ @.***> wrote:
Hi, @oushujun https://github.com/oushujun Thanks for developing EDTA. I am studying fall armyworm which is a lepidopteran pest. before using EDTA(1.9.8) to annotate assembly,i tried some methods to annotate this assembly.
- repeatmasker with repbase: SINEs: 0.61%, LINEs: 3.5%, LTR: 0.34%, DNA: 0.32%
- using repeatmodeler(2.0): SINEs: 0.89%, LINEs: 10.09%, LTR:1.91%,DNA: 1.54%, Unkown: 13.01% I used TEclass and ClassifyTE to classify Unkown consensus sequecne,most of consensus sequence was divided into DNA transposon.So i think percent of DNA transposon is much more than 1.54%
- using EDTA: SINEs: 0%, LINEs: 0.85%, LTR: 6.67%, DNA: 20.83% The change of DNA transposon is in my expections, but SINEs and LINEs is far from what I anticipated.
log.txt https://github.com/oushujun/EDTA/files/6644198/log.txt EDTA_Sf_1.e18701.txt https://github.com/oushujun/EDTA/files/6644199/EDTA_Sf_1.e18701.txt GCF_011064685.1_ZJU_Sfru_1.0_genomic.fna.mod.tbl.txt https://github.com/oushujun/EDTA/files/6644208/GCF_011064685.1_ZJU_Sfru_1.0_genomic.fna.mod.tbl.txt
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@BonesAQ I checked your output files and seems like there are some errors at the later steps. You may want to rerun the annotation step (--step anno --anno 1 --overwrite 0) with the current update (v1.9.9) to make sure it is correctly run.
Shujun
@BonesAQ I checked your output files and seems like there are some errors at the later steps. You may want to rerun the annotation step (
--step anno --anno 1 --overwrite 0) with the current update (v1.9.9) to make sure it is correctly run.Shujun
Thank you for your reply, i will take your advice to try it again.