How to improve the BUSCO score of the resulted predictions?

[bioinformaticspcj]

Dear the authors:
Thanks for developing such an useful program. I recently tried to annotate a lizard genome with 2Gb in size using TSEBRA. However, I found that the predicted gene annotations had very low BUSCO score as follows:

BUSCO was run in mode: proteins
C:70.3%[S:68.1%,D:2.2%],F:10.2%,M:19.5%,n:2586
1818 Complete BUSCOs (C)
1762 Complete and single-copy BUSCOs (S)
56 Complete and duplicated BUSCOs (D)
265 Fragmented BUSCOs (F)
503 Missing BUSCOs (M)
2586 Total BUSCO groups searched
I have used two different tissue RNA-seq data to run braker1 and a close species' proteins to run braker2 and combined them by TSEBRA with default parameters. Could you be kind to give me some advance to improve?

Thanks again and looking forward to your help.
Best,
Bob

[LarsGab]

Hi Bob,

TSEBRA isn't developed in this repository and the version here is not up to date. Please use TSEBRA instead.

Unfortunately, there can be several reasons for low BUSCO values. First, try again with the latest version of TSEBRA and, also, make sure that you use the latest version of BRAKER (and the associated software). Another reason for the low accuracy could be that the BRAKER runs were not successful. Make sure that they were run without errors and that the result has high accuracy. It could also be that the default configuration of TSEBRA is not working well for your case. Adjusting it manually is a bit difficult, but if you want to try it yourself, you can read about it in detail in the paper and in the readme file of TSEBRA.
However, the reason for the low BUSCO scores might be something else I didn't think of, or something very specific to your species or your input data.

Best, Lars

[bioinformaticspcj]

Dear Lars, Thanks for your valuable advice. I have tried the latest version of TSEBRA and BRAKER. The BUSCO score have improved a lot but I still have some questions. The results are as fellows: braker1:  C:96.1%[S:80.3%,D:15.8%],F:1.8%,M:2.1%,n:2586 braker2 prothint:  C:62.6%[S:52.0%,D:10.6%],F:16.0%,M:21.4%,n:2586  braker2 GenomeThreader:  C:54.9%[S:47.3%,D:7.6%],F:24.4%,M:20.7%,n:2586 TSEBRA:  C:93.4%[S:89.5%,D:3.9%],F:2.9%,M:3.7%,n:2586 Question1: The BUSCO score of braker2 is still very low even I uses different aligners. I just used three closely relative species peps to run braker2 following the examples. I do not kown why. Could you give me some advice to improve it? Question2: The TSEBRA resulted 47 953 predicted genes, which I think is much more than expected. Do you think I should alter the config file to remove some genes? If so, I am afraid the BUSCO score will decrease. Could you give me some suggestions? Thanks again. Best, Bob

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------------------ 原始邮件 ------------------ 发件人: "LarsGab/TSEBRA" ***@***.***>; 发送时间: 2022年6月1日(星期三) 晚上7:59 ***@***.***>; ***@***.******@***.***>; 主题: Re: [LarsGab/TSEBRA] How to improve the BUSCO score of the resulted predictions? (Issue #2) Hi Bob, TSEBRA isn't developed in this repository and the version here is not up to date. Please use TSEBRA instead. Unfortunately, there can be several reasons for low BUSCO values. First, try again with the latest version of TSEBRA and, also, make sure that you use the latest version of BRAKER (and the associated software). Another reason for the low accuracy could be that the BRAKER runs were not successful. Make sure that they were run without errors and that the result has high accuracy. It could also be that the default configuration of TSEBRA is not working well for your case. Adjusting it manually is a bit difficult, but if you want to try it yourself, you can read about it in detail in the paper and in the readme file of TSEBRA. However, the reason for the low BUSCO scores might be something else I didn't think of, or something very specific to your species or your input data. Best, Lars — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>