Reconstruction of complete gene cDNA from Trinity output

Question

[drtamermansour]

I am done with transcriptome assembly for a non-reference plant using Trinity. The final Trinity.fasta file has more than 70,000 contig. These contigs must include different isoforms or ESTs for the same genes. I want to merge those isofoms to generate a more complete gene cDNA. I can see that EGasselmbler is exactly doing what I want to do but my Trinity out but is ~100Mb and the webserver failed to upload. Can anyone recommend another software to do this job?

P.S. I tried using corset. It cluster the overlapping transcripts together but it did not give me the complete gene cDNA.

Thank you in advance