title: RNA-Seq of mz-17 at 24 h fermentation
design: Using Agilent 2100 Bioanalyzer ( Agilent RNA 6000 Nano Kit) to do the total RNA sample QC.Firstly, we filter the low quality reads, reads with adaptors and reads with unknown basesto get the clean reads.Then we assembled those clean reads into Unigenes, followed with Unigene functional annotation, SSR detection and calculate the Unigene expression levels. Finally, we identify DEGs between samples and do clustering analysis and functional annotations.We define raw reads as reads which containing low-quality, adaptor-polluted and high content of unknown base(N) reads additionally, these noise reads should be removed before downstream analyses. We use Trinity to perform de novo assembly with clean reads ( PCR duplication removed in order to improve the efficiency), then use Tgicl to cluster transcripts to Unigenes.