How to complete incomplete gene seqs using short read blast on NCBI

[lan_ub]

Here is my question:

I have a bunch of incomplete genes (cds only). Those gene sequences were obtained by mapping HiSeq reads to a reference genome. Now we want to mine from more short illumina reads to fill those gaps in each gene (probably one gene at a time?). Those short reads are only available in NCBI SRA (NCBI developed a new tool to blast against illumina reads. So we have access to illumina data blast). I want to know how I can achieve this goal.


I'm new to bioinformatics. So please explain as much detail as you can. Or please give me related paper links. I really appreciate!