I am hoping someone might be able to help me trouble shoot some issues I am having building an assembly which I would like to use as a reference for DE analysis. As the title states, I am using trinity and I am getting way too many transcripts. Before I go any further I will state that I have read the article "There are too many transcripts, what do I do?" but I think my problem is a bit beyond the scope of that post.
I am trying to build a de novo transcriptome assembly using pooled samples of sea urchin larvae (four samples representing one sample per four treatment levels). I am getting around 800,000 transcripts where I would normally expect to get around 70,000 to 100,000 for similar data sets. I know that at least part of the issue is that I have lots of duplicate genes/isoforms due to the nature of the samples (many pooled individuals), however this still seems extreme. I have tried collapsing my assemblies using Grouper and CD-HIT but the assemblies are so large that collapsing still produces very large assemblies. Does anyone have any suggestions?