I have 454 Roche transcriptome assembly results. It is a single transcriptome. It is assembled "de novo". Much recently a very closely related genome was published. I have compared some of our assembled transcripts with available complete CDS & I found the assembled transcript query coverage was not more than 60%. So I felt "reference assembly" could increase the "query coverage" than the "de novo assembly". I have 2 folders in the output file given to us by the company, they are 'sff' and "assembly". I cannot find a fastq file. Do I really need fastq file for assembling? I have .qual, .fna &. ace files. Are these files along with "new genome" enough for re-assembly ?
Based on the previous answers posted here I have intended to to check out Cufflinks & Scripture, anyway I need suggestions that could help do things better!
Supplementary question-Since I have only single transcriptome, is it possible to do statistical analysis for Gene Ontology results ?, because in this case the GO results will be based on available "contig count" !