I have elaborated a de novo transcriptome assembly by means of Illumina sequencing output with more than 300 million reads. I am now validating some gene models and looking for new isoforms in that assembly using blastn searches. I take into account the sequence identity and the coverage of the blast output to validate gene models. In some cases, I find a match between my sequence and one transcript from the assembly (sequence identity >95% and sequence coverage >90%), which confirm that my gene model would be correct and the expression of this gene in the studied conditions. However, in some cases I find a perfect match but it is partial e.g. the transcript from the assembly covers only 50% of my sequence. Could I consider this gene as expressed in the experimental conditions?
Thanks
Jose