How can I get GTF file for TE annotations from Helicoverpa armigera?

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3.1 years ago

pavelasquezv ▴ 50

Hi all,

I hope post finds you well

I need a GTF file for transposable elements annotations from Helicoverpa armigera genome. The species is not available in any database (UCSC RefSeq, Ensembl, iGenomes). Please, I would appreciate if someone can tell me how I can make the annotation myself and send me an example that I can follow.

Many thanks,

All the best Alex

genome workflow database pipeline • 973 views

ADD COMMENT • link 3.1 years ago by pavelasquezv ▴ 50

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I don't think you can find a ready-made copy. Annotation is the most expensive operation in the genome sequence for a reason. May want to look at this for possibilities to identify your own: https://www.biostars.org/p/379825/

ADD REPLY • link 3.1 years ago by GenoMax 141k

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Many thanks for your reply GenoMax. I understand, the truth is, I would like to know what is the best way to get GTF file for transposable elements annotations from Helicoverpa armigera. The example that you send me are very well. Many thanks!

ADD REPLY • link 3.1 years ago by pavelasquezv ▴ 50

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