*4.5. Novel Gene, Alternative Splicing and Enrichment Analysis*

When using Cuffcompare algorithm from Cufflinks software in mapping, reads that could not be mapped to the reference genome and the transcript FPKM ≥ 10 in any single sample were deemed as novel genes. For alternative splicing (AS) screening, the BAM files were processed by Cufflinks program to generate assembled transcripts followed by Cuffmerge algorithm to the final transcriptome assembly, which was subjected to Astalavista (version 3.1) algorithm to reveal AS [19,47,48]. Functional enrichment analysis of gene ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were by String 10.5 [49].
