EDTA
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oushujun
Extensive de-novo TE Annotator
When I installed the EDTA 2.0.0, I tried to run it. But there is something wrong in the step of the TIR. Is this the version problem of the python...
I see many people have had the same error message I received: Error: The RMblast engine is not installed in RepeatMasker! This is despite installing in the recommended way that...
Hi, Mr. Ou The proportion of repetitive sequences in the cotton genome annotated using the panTE library was 10% higher than that of EDTA. The results of this panTE library...
Dear @oushujun , Thank you for developing this useful tool. I have run it successfully and found that SINEs and LINEs could't be identified based on structure features. However, we...
https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation Generate de novo TE library for each genome and perform initial annotation. Is it necessary for --anno 1 for this step?
Basically the title. Here is the weird lines from the gff3 file... ``` 15593 EDTA repeat_region -2 3598 . ? . ID=repeat_region_23903;Name=TE_00012818;Classification=LTR/unknown;Sequence_ontology=SO:0000657;ltr_identity=0.9733;Method=structural;motif=TGCA;tsd=TTAAT 15593 EDTA target_site_duplication -2 2 . ? ....
Dear Shujun, Thanks for excellent tool! I have following questions when I try to classify my TE dataset and notice part of repeat_region also classify as TE: 1. What's different...
Hello, Thanks for developing this comprehensive TE discovery pipeline. We are currently aiming to annotate multiple plant genomes with TEs de novo, which have been taking a lot more computational...
Hello, Shujun! I successfully ran EDTA on a genome with a _sensitive_ setting. In the log file EDTA printed: ``` TE annotation using the EDTA library has finished! Check out:...
Hi Shujun, I encountered these problems when I try to run EDTA: Traceback (most recent call last): File "/home/umcentral18/miniconda3/envs/EDTA/bin/TEsorter", line 6, in from TEsorter.app import main File "/home/umcentral18/miniconda3/envs/EDTA/lib/python3.6/site-packages/TEsorter/app.py", line 25,...
