[maker-devel] comments on Incorporating cufflinks in maker

[Van Hoeck Arne]

Dear Rens and Carlson,
I would like to comment on Rens' question on adding transcript data into your annotation. Since I have no access to google groups, I try to contact you both via mail with, hopefully, the correct mail addresses.

I have tested Maker-P with multiple parameters, optimized 2 gene prediction tools (SNAP and augustus). Both give similarly results at which maker find around 17000 gene annotations. I also have RNAseq samples, and as a test case I also used Cufflinks output and processed with TransDecoder to select gene annotations. By using this approach, I end up with 25000 gene annotations. More or less, all the genes that Maker selected were also selected by the TransDecoder approach. So is it wise to include the information on the 8000 missing genes, based on optimized gene models? probably, there will some false positive in these 8000 missing genes, but with good criteria and models, it would maybe possible that maker can find more genes annotations.

Best regards
Arne

Hi maker team,

I am currently working on a project where we want to incorporate quite a lot of RNA-seq into our annotation. Currently I see two options:

Provide the cufflinks output as EST-gff
Process cufflinks output with TransDecoder (find ORFs, annotate UTR, etc) and provide this as either pred_gff or model_gff

What would you suggest, and what would be the required formatting for both options?

Thanks in advance,

Rens Holmer


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