Comments (6)
I used two ways of above with EDTA: pipeline1) using EDTA for genomeA; pipeline2) using the output TElib of pipeline1 as a curated library (--curatedlib), and rerun EDTA for genomeA again.
And here is the result statistics
Some types of TE with different num in these two output results. I checked some TE position and they are same.
Is it possible that reannotating genome by EDTA again is optional, or not need to reannotate again?
Best!
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Thank you, Shujun.
I run pipeline1 and pipeline2 both with --anno 1 previously. I'll just use pipeline1 (with --anno 1) to save time.
Best!
Hello, Your pipeline 2 step 2 can be merged into step 1 if you specify —anno 1 in your step 1. This annotation is necessary to identify copy numbers of each family.
Your results are pretty consistent. The variations can be considered uncertainty of TE annotation. Please check the wiki.
Best, Shujun
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Hi @oushujun,
I have some confusion about the panEDTA pipeline. It seems that panEDTA runs EDTA on each genome individually and then merges the EDTA TE libraries from each genome. Considering that genomes constituting the panGenome have a significant proportion of shared conserved sequences (core genome), why not first construct the panGenome from different genomes and then use EDTA to identify and annotate TEs on the panGenome?
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Hi, Shujun.
I am sorry to bother you again.
I downloaded some genome and cds data from NCBI, and want to annotate them using EDTA.
Some homologous chr sequence in different genomes are inverted. And I plan to use the reverse complement sequence of these chr to ensure the consistency of strand. May I also need to use the reverse complement sequence of cds data in these chr? Or primary cds data is ok and strand INFO have no impacts on TE annotation?
Thanks!
Best!
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Related Issues (20)
- 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 3
- EDTA_2.2.x.yml seems not working HOT 7
- Concatinating CDS files for panEDTA HOT 1
- making the output gff3 valid HOT 4
- 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
- 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
- make_masked.pl Permission denied HOT 1
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