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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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calculate the LTR insertion time by EDTA #271

Closed tinyfallen closed 2 years ago

tinyfallen commented 2 years ago

Hi dear developer, The LTR_retriever accepts the -u parameter for LTR insertion time calculation while the EDTA not. The user have to recalculate by themselves. For my own, I'm afraid I may make mistakes in the calculation steps. So could you please do a favor to add the -u parameter to EDTA in the next update? Thanks a lot !

oushujun commented 2 years ago

Hello @tinyfallen,

This is a good suggestion. I will add -u in the next release.

Shujun

Chriswinefield commented 2 years ago

Hi Shujun, Just related to this I was wondering if the EDA output could be used to feed back into LTR_retriever with the -u flag to generate the insertion time calculation, or whether there is a suitable intermediate output file that we could use.

Like @tinyfallen having this flag in EDTA would be fantastic - cant wait for the next release :)

Many thanks Chris

oushujun commented 2 years ago

HI Chris,

Thank you for reminding me. Yes, this is on my to-do list and I will try to get it done soon.

Best, Shujun

Chriswinefield commented 2 years ago

Thanks Shujun,

Looking forward to the update in due course. In the meantime Is there a possibility of using one of the EDTA intermediate files to pop into LTR-retriever or would I be best just running the LTR-retriever pipeline independantly?

Kind Regards Chris

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From: Shujun Ou @.> Sent: Thursday, June 16, 2022 6:28:52 PM To: oushujun/EDTA @.> Cc: Winefield, Christopher @.>; Comment @.> Subject: Re: [oushujun/EDTA] calculate the LTR insertion time by EDTA (Issue #271)

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HI Chris,

Thank you for reminding me. Yes, this is on my to-do list and I will try to get it done soon.

Best, Shujun

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oushujun commented 2 years ago

Hi Chris,

You can run EDTA_raw.pl with the --type ltr parameter. Then essentially you will be just running LTR_retriever. You may also use the scn files located in the `raw/LTR/directory to run LTR_retriever with-inharvest`.

Shujun

oushujun commented 2 years ago

This parameter (--u) is added to the latest repo and release. Please allow a couple of days to reflect on the conda recepie. Please let me know if you have more questions.

Chriswinefield commented 2 years ago

Hi Shujun,

Many thanks for that addition - I will let you know how it goes in due course.

Kind Regards Chris

Chris Winefield Associate Professor in Plant Genomics and Molecular Biology

Department of Wine Food and Molecular Biosciences Faculty of Agriculture and Life Sciences

RFH, room 062 Engineering Drive P O Box 85084 Lincoln University Lincoln 7647 Christchurch New Zealand

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From: Shujun Ou @.> Sent: 23 June 2022 12:23 PM To: oushujun/EDTA @.> Cc: Winefield, Christopher @.>; Comment @.> Subject: Re: [oushujun/EDTA] calculate the LTR insertion time by EDTA (Issue #271)

Caution: This email originated from outside our organisation. Do not click links or open attachments unless you recognize the sender and know the content is safe.

This parameter (--u) is added to the latest repo and release. Please allow a couple of days to reflect on the conda recepie. Please let me know if you have more questions.

— Reply to this email directly, view it on GitHubhttps://github.com/oushujun/EDTA/issues/271#issuecomment-1163795280, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABYMLSVWWNI3VPU3ZVXAYUDVQOVA3ANCNFSM5XJYQKSQ. You are receiving this because you commented.Message ID: @.***>

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tinyfallen commented 2 years ago

This parameter (--u) is added to the latest repo and release. Please allow a couple of days to reflect on the conda recepie. Please let me know if you have more questions.

Dear teacher,

That's so fantastic!

Actually, I do have met some problems about the classification of TEs recently.

I found almost half of the final library labelled Unknown which seemed to come from the RepeatModeler steps. So I separately fed the lib to TEsorter and deepTE to perform classification, in which some sequence's classification may be contradictory with each other or the original result of EDTA.

Following comes my questions:

  1. Is it necessary to further classify the unknowns?

  2. The RepeatMasker's out file contains many overlaps between repeats in different repeat types. I found the EDTA's -anno result have a consensus number between the total and the sum of all types' percentages. Could you please tell me how does EDTA deal with the overlaps, or criteria to determine the overlapped genome sequence's classification destiny?

Maybe I should open a new issue to consult the questions, or you could just give me some brief suggestions, thanks!

Best~

tinyfallen commented 2 years ago

Dear teacher,

I saw the discussion in issue98 and found the genome.mod.EDTA.TEanno.split.gff3, thus I could conduct analysis using this file to exclude overlaps. Descriptions in detail about the outputs could be added into wiki or README if you would like to.

And I still have the interest to know how it accomplished and whether it is necessary to further classify the unknowns.

Wish to see a more powerful and comprehensive EDTA!

Thanks for your excellent work!

oushujun commented 2 years ago

Hi @tinyfallen,

Thank you for your suggestions. I have added the following Q&As to the wiki: https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A What's the difference between different GFF files? How to summarize TE annotation in my genome?

For unknown TEs, it's always recommended to classify them as much and accurately as possible, but this is challenging. You may use TEsorter, deepTE, or others to do so, and use --curatedlib to provide the updated library. Always keep in mind, that there will be misclassification.

Best, Shujun

tinyfallen commented 2 years ago

Many thanks dear teacher!

Best~