Identifying flanking LTR pairs about edta

[oushujun]

Dear Bryan,

Currently the full EDTA annotation pipeline is aggressively removing nested insertions and reducing the redundancy, which will result in a fragmented TE annotation. This could be the reason that you find the annotated TEs are not giving you the precise LTR region. I am working on resolving this issue, but alternatively, you can use the intact TE annotation file which contains the information you are looking for. It's located in the *EDTA.raw/ folder with the *intact.fa.gff3 naming.

Please let me know if this answers your question. Thank you for testing EDTA.

Best,
Shujun

[bryan-n-arch]

Hi Shujun,

I don't have this file in my "*EDTA.raw" directory (or at least I'm not seeing it) -- perhaps because I used an older version? Our library was built a few months ago.

I do, however, have a "*.pass.list.gff3". It seems like it contains the left and right flanking pairs reported by LTR retriever. Can I rely on this to derive the flaking LTR pairs?

I appreciate the help.

Cheers,

Bryan

[oushujun]

Hi Bryan, Yes this is the file you are looking for. I recommend you to update EDTA because of a recent major update, which will improve thd overall annotation accuracy. However, for intact LTR it is likely the same. Best, Shujun

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On Tue, Dec 10, 2019, 2:45 PM Bryan Naidenov ***@***.***> wrote: Hi Shujun, I don't have this file in my "*EDTA.raw" directory (or at least I'm not seeing it) -- perhaps because I used an older version? Our library was built a few months ago. I do, however, have a "*.pass.list.gff3". It seems like it contains the left and right flanking pairs reported by LTR retriever. Can I rely on this to derive the flaking LTR pairs? I appreciate the help. Cheers, Bryan — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#32?email_source=notifications&email_token=ABNX4NG3QH2XLLYACFZ7NB3QX75WZA5CNFSM4JXS2GTKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGQ4MSA#issuecomment-564250184>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NB6DBLZEWMJ5JER7MLQX75WZANCNFSM4JXS2GTA> .