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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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LINE and SINE #332

Closed bijendrabio closed 1 year ago

bijendrabio commented 1 year ago

Hello, Curious if there's a way to integrate additional SINE and LINE information to EDTA final TE library (*TE.lib.fa) file and run the final annotation step to generate the summary (.sum) file showing the information about added SINE/LINE composition.

I tried by adding the following opitions: --curatedlib *TE.lib_SINEadded.fa --step anno -anno 1 but got the blank results in .sum file. Kindly suggest!

Regards, B

oushujun commented 1 year ago

Hi,

Yes You can do it this way, but you will need to format the library in the RepeatMasker format. Please refer to the wiki page for more information.

Shujun

On Tue, Feb 7, 2023 at 8:56 AM bijendrabio @.***> wrote:

Hello, Curious if there's a way to integrate additional SINE and LINE information to EDTA final TE library (*TE.lib.fa) file and run the final annotation step to generate the summary (.sum) file showing the information about added SINE/LINE composition.

I tried by adding the following opitions: --curatedlib *TE.lib_SINEadded.fa --step anno -anno 1 but got the blank results in .sum file. Kindly suggest!

Regards, B

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/332, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NG5ULMIJVKJSSLJFF3WWJH7HANCNFSM6AAAAAAUT74GLE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

bijendrabio commented 1 year ago

Thank you @oushujun. Is there a way to update the final result of EDTA with newly identified SINE and LINE without the need to restart the EDTA from the beginning?.

oushujun commented 1 year ago

Yes, you can start from --anno 1 --step final --overwrite 1 to include SINE LINE results.

Shujun

On Mon, Feb 13, 2023 at 11:59 AM bijendrabio @.***> wrote:

Thank you @oushujun https://github.com/oushujun. Is there a way to update the final result of EDTA with newly identified SINE and LINE without the need to restart the EDTA from the beginning?.

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/332#issuecomment-1428296354, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBRLRS2CXVHRRQ7GVLWXJR6DANCNFSM6AAAAAAUT74GLE . You are receiving this because you were mentioned.Message ID: @.***>