Very high cross-replicate variability

This section assesses Cuffdiff's power and sensitivity when cross-replicate variability is extremely high. In such settings, substantial power should be gained by adding additional replicates to the experiment. The section includes up to 10 replicates in each condition. To highlight the benefit of added replication, and to make the simulation slighlty less onerous on our testing servers, we have also reduced sequencing depth to approximately 4 million paired end reads per replicate.

Estimation of expression values in a single condition

Genes

Transcripts

Estimation of expression values between conditions

Genes

Transcripts

True and false positives

Genes

Transcripts

DE TSS Groups

Differentially Spliced TSS Groups

Promoter Switching Genes