KatharinaHoff
commented
2 months ago This is very confusing. BRAKER3 works with both RNA-Seq data AND a protein database. BRAKER2 works with proteins only. However, I have seen the same confusion elsewhere, earlier this week. Is it possibly labelled incorrectly in Galaxy? If that is the case, please let me know (we do not maintain this ourselves, but we can contact the authors of the Galaxy workflow).
Use BRAKER3 if you have both RNA-Seq and protein data. (If it is labelled incorrectly in Galaxy... well... use the tool that allows upload of both data, for now). BRAKER1 as well as the BRAKER1/BRAKER2/TSEBRA approach do not have as high accuracy as BRAKER3. See https://genome.cshlp.org/content/early/2024/05/28/gr.278090.123.abstract
On Wed, Sep 18, 2024 at 9:25 AM RacheliHadjez @.***> wrote:
Hello, I am currently working on the genome annotation of a myxozoan species and would like to use BRAKER for this purpose. Based on a BRAKER tutorial, I understand that the optimal approach for my species is to run BRAKER1 with RNA-seq data and BRAKER2 with protein data, and then use TSEBRA to combine the results from both runs.
However, I noticed that on the Galaxy server, only BRAKER2 and BRAKER3 are available, and BRAKER2 has an option to input both RNA-seq and protein data. My question is: can I use BRAKER2 with both RNA-seq and protein data instead of running BRAKER1 separately, and then use TSEBRA on the results? Or does it specifically need to be BRAKER1, requiring me to run it on a Linux server?
Thank you in advance for your help! Rachel
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RacheliHadjez
Hello, I am currently working on the genome annotation of a myxozoan species and would like to use BRAKER for this purpose. Based on a BRAKER tutorial, I understand that the optimal approach for my species is to run BRAKER1 with RNA-seq data and BRAKER2 with protein data, and then use TSEBRA to combine the results from both runs.
However, I noticed that on the Galaxy server, only BRAKER2 and BRAKER3 are available, and BRAKER2 has an option to input both RNA-seq and protein data. My question is: can I use BRAKER2 with both RNA-seq and protein data instead of running BRAKER1 separately, and then use TSEBRA on the results? Or does it specifically need to be BRAKER1, requiring me to run it on a Linux server?
Thank you in advance for your help! Rachel