EDTA

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TIR-Learner results aren't DNA transposons

4

Hi Shujun, I'd previously used EDTA when you included MITE-Tracker (or MITE Hunter? I'm not sure which) and got some decent results for a _de novo_ yeast species. Having seen...

coopergrace

identify SoloLTR

12

Dear Shujun, Can you give us a script to identify soloLTR based on the annotation file of EDTA,the script of LTRretriver to identify solo_LTR can hardly suit the outcome for...

Bioyu721

Issue with Names between output files

4

Hi, I ran the program successfully with perl EDTA.pl --genome *.fa --anno 1 --threads 45 However, looking at the Names in *.TElib.fa they don't all match with the Name column...

natalialplg

ERROR: No candidate is found in the file(s) you specified.

2

Hi shujun, When I'm running the EDTA process, I'm getting an error that I can't fix. I have pasted my log file as below, I hope to get your help....

caixu0518

questions about the outputs

1

Hello Dr. Ou, Thank you for the tool and tutorials! I have some questions about the outputs. In the `colcen.fna.mod.LTR.intact.gff3` file, it showed that 1662 intact LTRs were detected (same...

XinyiLiuLMU

RepeatMasker error: mdb_env_open: Cannot allocate memory

5

Thank you for this great tools ! I have met some problem, could you help me ? I installed EDTA through `conda`, by two ways: ``` #the first way git...

jun3234

ERROR: Raw TIR results not found in Fhispida.fasta.mod.EDTA.raw/Fhispida.fasta.mod.TIR.raw.fa

5

Hi, shujun I recently run the EDTA pipeline(v2.0.1) on the Ficus hispida using the following command > As the EDTA was running successfully on my arabidopsis species, the pipeline was...

xuzhougeng

ERROR: blastn is not exist in the BLAST+ path

1

Hello! I am running the cleanup_nested.pl as following: perl cleanup_nested.pl -in file.fa -blastplus /path to blast conda environment But I have this error: ERROR: blastn is not exist in the...

ericadinatale

Annotating draft genome with thousands of sequences

7

Dear Shujun Ou, Thank you for developing this excellent tool; I have been successfully using it for a couple of years. Currently, I am annotating draft genome assemblies (scaffold-level) of...

bvs

Can EDTA produce the non-redundant and matched gfffile of genome.mod.EDTA.TElib.fa?

3

Hi, Mr. Ou I used following command: perl EDTA.pl --genome HFTH1.all.chr.fa --sensitive 1 --evaluate 1 -t 10 Then I got HFTH1.all.chr.fa.mod.EDTA.TElib.fa, HFTH1.all.chr.fa.mod.EDTA.intact.gff3 and other files. In order to get the...

2eYu