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JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
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Does it necessary to have an assembled genome to run PiRATE pipeline #37

Closed majie5976 closed 4 years ago

majie5976 commented 4 years ago

Hi @JBerthelier , Hope all is fine with you. Before running PiRATE pipeline I just want to confirm that, Does it necessary to have an assembled genome to run PiRATE pipeline. Because species I'm working on not possible to have an assembled genome due to large genome size. Can I use approach 4 (build repeated elements) in step one, then proceed the following steps as it is. The questions why I'm asking because I checked the final step TEannot there is two input requirements

  1. genomic Sequences (Enter the genome assembly)
  2. TE Library (the manually constructed TE Libraries) If I'm not worng. Your suggestions would be appreciated ! Sorry due to Server link down problem this issue gets duplicated, allow me to delete one of them. Thanks Regards, Majie
JBerthelier commented 4 years ago

Dear Majie,

Thanks for your message and interest about PiRATE.

PiRATE is very flexible, you can only use the tools that are interesting for your study. It's a kind of platform with a of lot of tools to help you to achieve what you want.

Thus, you don't need to have a genome assembly to use some tools.

For exemple if you want to know what types of TEs are in the genome of the species you are studying, you can only use the tools of the approches 4 (detection step), and then use PASTEC (classification step). You will got a library of TEs that are in the genome.

But, because you do not have a genome assembly you will not use TEannot (annotation step).

Hope this will help you,

(no problem for the duplicate)

Best regards,

Jeremy

majie5976 commented 4 years ago

Hi @JBerthelier , Got it, Many Thanks.