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the pipeline about panEDTA #436
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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
…On Thu, Feb 22, 2024 at 9:56 PM Hui ***@***.***> wrote:
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
image.png (view on web)
<https://github.com/oushujun/EDTA/assets/77773766/80e110d2-b8ec-408e-8f17-f0c67101b0af>
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.
|
Hi @oushujun, |
Yes, you may do that. Be aware that the graph pangenome may present
variable sequences to you without the adjacent sequences, the latter are
needed for EDTA to determine the authenticity of a structurally intact TE.
Best,
Shujun
…On Fri, Feb 23, 2024 at 1:14 AM Kang Hu ***@***.***> wrote:
Hi @oushujun <https://github.com/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 downloaded some genome and cds data from NCBI, and want to annotate them using EDTA. Thanks! |
Hi, Oushujun!
I have some animal genomes and want to annotate them by panEDTA. But now, I am confused about the some pipeline of panEDTA.
I read some others' issues about panEDTA, and they seem that:
But I read the example you provided (https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation)
It seems that:
So, my question is about,should I reannotate the genome again with their TEblib in step2?
Thanks!
Best Wishes!
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