Trinity min_kmer_cov

A high min_kmer value was used to reduce noise in the assembly and to identify only transcripts that were relatively highly expressed. At lower min_kmer values, intron retention was observed, possibly from incomplete splicing of preWmRNAs. The vast majority of examples of potential intron retention showed very low expression levels based on post alignment of the RNASeq reads. As such, increasing the min_kmer value prevented many such cases from being included in the initial inchworm assembly step. The primary drawback of this approach was that some lowly expressed transcripts were no longer assembled and other transcripts with low expression became more fragmented.