I'm trying to predict the exact intron/exon structure of a gene of interest. Available I have the genomic sequence and the transcriptome of the organism at NCBI's SRA. I tried it using the SRA BLAST tool provided at NCBI but I can't seem to get it right. Is there a simple way to assemble the short reads with the template of the genomic DNA? I just need to do this process with one gene.
Thanks in advance