Hi,

why we performed cufflinks and what does the assembled transcripts mean? I read the protocol, if I am right that cufflink will provide a reference transcriptome on which the reads can be aligned and enables use to calculate the expression level of genes???


Cufflinks builds the transcriptome for a sample. Transcripts are assembled using aligned reads which you provide in the form of a bam file. It also quantifies the assembles transcripts. Reference transcriptome is provided if it is available for that species. It helps cufflinks in building the transcriptome of the sample.