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JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
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TEannot query #46

Closed pwkooij closed 4 years ago

pwkooij commented 4 years ago

Hi

I have a quick question regarding TEannot. I just did the first run, but in the tutorial you do a second run. Which of the output files from the first run do you use for this?

Cheers Pepijn

JBerthelier commented 4 years ago

Dear Pepijn,

The author of REPET (TEdenovo, PASTEC, TEannot) advised me to do a second run of TEannot using the Full length copy (FLC).

The sequences in the Full length copy, become your final TE library for the TEannotation. This helps to reduce the redundancy of the reference TE sequences.

Cheers,

Jeremy

pwkooij commented 4 years ago

ok, thanks for the answer, Jeremy, much appreciated!

Lukanyo12 commented 4 years ago

Hello @ JBerthelier, is there any script for removal of redundancy sequences in CD Hit_est, or we are expected to eliminate the redundant sequences our selves after the run/clustering

Best Lukanyo

On Tue, 11 Aug 2020, 10:21 PM pwkooij, notifications@github.com wrote:

Hi

I have a quick question regarding TEannot. I just did the first run, but in the tutorial you do a second run. Which of the output files from the first run do you use for this?

  • Full length copy
  • Full length fragment
  • TE with one copy and more

Cheers Pepijn

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