In a scenario where we are to compare paired-end RNA-Seq data from an instance of technical replicate, my understanding is that the Cufflinks output (pointedly transcripts.gtf) from each condition (mock-treated) will represent specific reads; until they are merged together to actually superimpose and render a collective read-gene overlap count matrix. This is the premise for Cuffdiff to unravel differentially expressed genes.
Question: From the revered Tuxedo Suite for NGS data analysis, under what circumstances could the usage of Cuffmerge be thwarted?
19 months ago by
Shaurya Jauhari • 40
Shaurya Jauhari • 40 wrote:
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