Pipeline is as follows: Trinity (min_kmer_cov 3, min_glue 3), CDHITEST followed by CAP3 (for redundancy removal). RSEM for calculating expression values, followed by EdgeR for differential expression.
After redundancy removal I have about 300,000 unigenes, which seems still high (joined cap3 contigs and singletons).
Now my problem is in the FPKM values for RSEM, I seem to be getting a lot of 0 values for transcripts, and for differential expression analysis (fold change 2, fdr =0.05) I am getting around 100 differentially expressed genes between some conditions. I was expecting a lot more. In some comparisons there are even only 10-30 differently expressed genes.
Anyone have any idea what could be wrong? I am a bit of a noob to transcriptomics. The RSEM reads provided between 85-95% alignment success.