[maker-devel] maker annotation with cufflinks output

[dhivya arasappan]

Hello,

I am trying to annotate a 200 mb plant genome for which I have a very  
good assembly.

I tried to denovo assemble RNA-seq data using trinity and ran maker  
using my genome assembly and the trinity results.  I did not get as  
many transcripts as expected, around 10,000 transcripts.

So, I decided to try a different approach.  I did a genome assisted  
assembly of the RNA-seq data using tophat/cufflinks. This pipeline  
generated 21,000 genes, 29,000 transcripts.  I then ran maker using my  
genome assembly and the cufflinks result.  I get much less number of  
transcripts as a result.

If cufflinks found 29000 transcripts by mapping to the genome, I'm  
confused as to why maker is not finding the same.

Any suggestions would be appreciated.

Thanks
Dhivya