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Anyone with experience in the TE-annotation package REPET?

Hi, is there anyone out there who has experience in the TE-annotation package REPET? It would be nice to get some help in order to avoid the largest pitfalls.

Thanks
Kajsa

transposable-elements annotation repet
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updated by Ram Ram • written by kajsa.himmelstrand • kajsa.himmelstrand

2 answers

Here is an install guide for the SGE queuing system, just remember to do a system reboot.

https://scidom.wordpress.com/2012/01/18/sge-on-single-pc/

In the MySQL setup, if you forget to set the database schema to MyISAM AFTER you try to run REPET, you must go back and delete the tables in MySQL and restart from scratch. The syntax is on google.

Additionally, I have been receiving empty outputs from the GROUPER clustering program. Not sure if this is related to my fragmented assemblies, but you can try to troubleshoot by running the commands yourself without the SGE system by examining the system command calls in the python script created inside of the working directory.

It is worth the trouble, at least in regards to the model organism reference I have succeeded with. 4x the amount of repeats in the library than from RepeatModeler.

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updated by Ram Ram • written by muppetleague • muppetleague

Hi,

I am trying to install the REPET v3 using the docker container I am following the documentation: https://hub.docker.com/r/urgi/docker_vre_aio

However, when I want to configure the tool: cp $REPET_PATH/config/TEdenovo.cfg .

I receive an error: cp: cannot stat '/config/TEdenovo.cfg': No such file or directory

can anyone guide me on how to make it work?

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written by mthm • mthm

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