[maker-devel] basic question on maker

[hcma]

Hi,

I would like to include a de novo assembled transcriptome assembly for 
running maker. The organism i am working with is fly and I am wondering 
what is the best way to do this?

Do I need to get the input files for running Repeatmasker or just set:

model_org=all

What's the best protein sequence file to use?

is ' uniprot_sprot.fasta' ok?


Some people use Trinity transcriptome assembly to generate a train set 
for Augustus and then run maker again, is this a better way than running 
maker just once?


Thanks for your time and any comments will be greatly appreciated.

Best Regards
Karen