Hi!
I am trying to annotate the transposable elements of a fly genome. But I am particularly interested in doing a comprehensive work.
I am using programs like RepeatModeler and REPET to find and classify transposable elements. I am using more than one program to maximize the sequences recovered.
My problem is I don’t know how to merge the outputs. First I did it with RepeatMasker, using one of the libraries as a genome and another as a library and vice versa. And then going through the outputs trying to find the most complete and better classified copy. But it is a very long process and I am sure there are better options.
Now, I am thinking of letting RepeatModeler build the consensus, just concatenate all the libraries and use them as a genome. The drawback is I lose the option to keep the better classification.
Did you have a similar problem? Or do you think the programs are not that different to deserve the effort of using more than one?
Thank you for your help
Nuria
I am trying to annotate the transposable elements of a fly genome. But I am particularly interested in doing a comprehensive work.
I am using programs like RepeatModeler and REPET to find and classify transposable elements. I am using more than one program to maximize the sequences recovered.
My problem is I don’t know how to merge the outputs. First I did it with RepeatMasker, using one of the libraries as a genome and another as a library and vice versa. And then going through the outputs trying to find the most complete and better classified copy. But it is a very long process and I am sure there are better options.
Now, I am thinking of letting RepeatModeler build the consensus, just concatenate all the libraries and use them as a genome. The drawback is I lose the option to keep the better classification.
Did you have a similar problem? Or do you think the programs are not that different to deserve the effort of using more than one?
Thank you for your help
Nuria
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