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urgi-anagen / TE_finder

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.
https://urgi.versailles.inra.fr/Tools/REPET
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We still need to annotate duster results? #2

Closed xiekunwhy closed 2 years ago

xiekunwhy commented 2 years ago

Hi,

I can't find any relationship infomation between DUSTER results and TE library sequences using test data, so we still need to annoate Duster results?

Or is there an easy way to know TE classes in DUSTER results?

Best, Kun

hquesneville commented 2 years ago

Dear Kun,

DUSTER is made to detect very old TE which are difficult to detect by other means. They are often so old and degenerated that it is difficult to see the type of TE the sequence belongs to. Consequently it is not able to determine the class.

Best,

Hadi

Hadi Quesneville Directeur de recherche / Research director Administrateur des Données Algorithmes et Codes de la recherche (ADAC) / Chief Data Officer

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Le 7 juil. 2022 à 09:10, xiekunwhy @.**@.>> a écrit :

Hi,

I can't find any relationship infomation between DUSTER results and TE library sequences using test data, so we still need to annoate Duster results?

Or is there an easy way to know TE classes of DUSTER results?

Best, Kun

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xiekunwhy commented 2 years ago

Dear Hadi,

The not so old TEs are also included in duster results, right? So I need to annotate the duster results using some other tools like censor or repeatmasker to get the class information of those not so old TEs, I will do that.

Best, Kun