fill gaps in genome by transcripts

[neurospora]

Hi,
I have scaffold and transcripts assembled by us,but there are so many gaps in scaffold ,some of which are small. I am trying to reduce the gaps by transcripts and predict CDS from scaffold using transcripts as reference.
So,I hope to get some advice and methods from experts.
thank you!
best wishes!

[HESmith]

RNA-Seq data has been used to improve the assembly of a nematode genome: see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990000/ for the details.

[neurospora]

Hi,HESmith,
Thank you for your suggestion!
I will read the paper to get what I want to know!
Best wishes!