Public RNAseq as evidence for BRAKER?

[V-JJ]

Hi!

I have the following question. I want to annotate a publicly available genome using proteins and RNAseq.

• Proteins: one of the available datasets such as arthropodaODB (In absence of a better alternative)
• RNAseq: available NCBI data. Given that the available data may com from different individuals and / or tissues, what would you recommend or strongly advise against?

For instance, let's suppose that there are RNAseq data obtained for

• The whole organism and/or...
• Tissues specific sequencing

What would you do? Any recommendation or advice is appreciated,

Thanks V

[LarsGab]

Hello,

I don't think it's an issue if the RNA-Seq data comes from different individuals or tissues. In our benchmarking, we selected RNA-Seq libraries randomly, without considering the source individuals or tissues. However, it is important to use enough data, we used ~6 RNA-Seq libraries from the SRA per species.

Best, Lars

[V-JJ]

Hi!

Understood, clear know! Thanks for you help. Best, V