Fig. 1
From: Identification of alternative splicing events by RNA sequencing in early growth tomato fruits
The flow chart of gene expression analysis and AS detection used in this study. Following mapping of the reads to the reference genome (version ITAG2.5), the mapped reads were assembled by Cufflinks. The Cufflinks tools Cuffdiff was used for identification of differentially expressed genes at gene level and differential alternative splicing. Cuffnorm was used for estimating expression levels of individual transcripts assembled by Cufflinks (isoforms). Then a very conservative cutoff (FPKM > =1 and fold change (FC) > =4) was used to select differentially expressed splice variants. AS events were extracted from the merged (fruits) or individual (seedlings and flowers) GTF generated by Cufflinks using the web server tool ASTALAVISTA. For NTR analysis, transcripts assembled by Cufflinks (merged GTF file from all samples) were compared to the annotated ITAG2.4 transcripts and then novel transcripts were analyzed by Sequencher