We have two sets of contigs assembled by Trinity and Oases (on S.pombe). We would like to compare the performance of them in terms of full length transcripts. I understand that a transcriptome depends on the condition when it was sequenced. But is there some annotated transcripts are relatively "complete"? By "complete" I mean it captures splicing forms of the genes.
I have found Pombase, which provides genome and genes but no transcripts. Also there is a Science paper from Broad Institute, which provides transcripts in FASTA format (http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiHome.html). Is this dataset good for my application? Or any other one is better?