The BUSCO assessment of the MAKER annotation results shows a low completeness

Question

[mut]

I performed the first round of MAKER annotation for my genome using RNA-seq and homologous proteins. The BUSCO assessment of the resulting proteins showed a completeness of only 64%. I then selected genes with AED less than 0.1 to train Augustus and SNAP, and performed a second round of MAKER annotation. However, the BUSCO assessment of the resulting proteins is still very low, only 53%. Why is this happening?

[Abieskawa]

What did you do before MAKER annotation, did you do repeat masking?

[mut]

I used RepeatMasker independently and generated a GFF3 format file, which was used as input for MAKER

#

"I would like to know if it is normal that the BUSCO evaluation of the proteins and transcripts output from the first round, where I only used EST and protein for annotation, is only around 60%. When I use the output from the first round to train de novo prediction tools such as Augustus and SNAP and run the second round of MAKER, the BUSCO evaluation of the proteins is still very poor. Why is that?"

[Ram]

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

[Abieskawa]

I think 60% is way too low

[Michael]

What's the completeness of the genome alone?

[mut]

BUSCO assesses the completeness of the genome as 96%.

[lieven.sterck]

Then clearly something is wrong with the annotation by MAKER .. (as this number indicates that the built-in annotation process of BUSCO is out-performing MAKER)

[Abieskawa]

I did not try Maker before, but my colleagues did. I am not sure the BUSCO, but number of the predicted genes was around 50,000 in Tilapia. We cannot sure it is the problem of Maker or the repeat masking process (he did not apply repeatmodeler build custom repeat database first), and there are more pipeline tools can be applied, so we stop using it now. You can try:

1. give up Maker, use Braker or Ginger
2. Inspect the result of repeat masking, if it masks too much or other problems

[samuel.a.odonnell]

Can you try without rnaseq data?

[Sony]

How did you run BUSCO? and what database of BUSCO did you use ? What version of MAKER ?

[mut]

I used the BUSCO embryophyta_odb10 database and Maker v3.01.03