Quantification for transcirpt without reference genome.

[huan]

Hello, every one!
I have got the transcript downloaded form NCBI. Also we have got the RNA-Seq data from illumina platform. Now we want quantify the transcript with short reads. Since we don't have reference genome, several method can be considered:
1. RSEM( bowtie+RSEM)
2. RSEM (bowtie+eXpress)
3. blat +counting reads mapped to full-length transcript(mutiple mapped reads?)

Q1: As I know, RSEM can need a file containing 'gene(tab)transcript' identifiers per line (--gene_trans_map). Since we have no idea about the gene and transcript information, so will the result be mattered?
Q2: If I use blat to mapped the short read, How can I deal with the multiple mapped reads?
Q3: after all, which method is best for quantification with no reference genome? Or is there any better method for the transcript?

Thanks a lot for any apply!