Comments (4)
@oushujun Thanks for that.
Just the four listed above - two of which you listed again (Identity, Method).
I'll let you know if anything else crops up when since I'll be testing dozens of genomes in the next few weeks.
Colin
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Thank you @colindaven
Have you tried: gt gff3 -retainids -tidy
? Sometimes I use this command to fix issues like the one you have mentioned.
from edta.
Hi @GallVp thanks for the tip, but I'm not too keen on the output.
It seems to do the job, but introduces "###" after every line or edit, and almost doubles file length
91933 AT_edta_original.gff3
182608 AT_tidied_by_gt.gff3
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@colindaven Thank you for the suggestion. It's a simple fix in the source code. Did you find anywhere in the gff3 output that needed to be fixed? For example, ID, Name, Identity, Method, TIR, TSD
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Related Issues (20)
- LTR retriever fails HOT 5
- LINE search takes much longer compared to other steps HOT 3
- resubmit jobs HOT 1
- Rerun EDTA 2.2.0 with results from older version HOT 8
- PanEDTA Line Detection HOT 1
- 2024-01-30 02:12:48,620 -WARNING- Grid computing is not available because DRMAA not configured properly: HOT 1
- TIR filtration HOT 3
- EDTA crahed after no SINE found HOT 6
- Benefit of using panEDTA HOT 1
- Testing output HOT 4
- EDTA_2.2.x.yml seems not working HOT 7
- Concatinating CDS files for panEDTA HOT 1
- Exploring the Discrepancies between TEanno.gff3 and TElib.fa HOT 2
- Inflated TE counts and masked bp in EDTA annotation after removal of part of the genome HOT 3
- panEDTA for metazoans HOT 5
- the pipeline about panEDTA HOT 6
- Two genomes LTR result file has 0 bp, while the others are not. HOT 3
- Use of uninitialized value $iden in numeric lt (<) at /home/data/ycy/sofw/EDTA/util/TE_purifier.pl line 184. HOT 2
- ERROR in TE annotation stats HOT 9
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