Hi,
I have a paied-end RNA-seq study like below
- Arabidopsis-heat for 2 hours
- Arabidopsis-control for 2 hours
- Arabidopsis-heat for 8 hours
- Arabidopsis-control for 8 hours
- Arabidopsis-heat for 24 hours
- Arabidopsis-control for 24 hours
I am running cuffdiff like below
cuffdiff -o diff_out -b genome.fa -p 8 -u merged_asm/merged.gtf 204.bam, 205.bam, 206.bam, 207.bam, 208.bam, 209.bam
at first telling
Warning: No conditions are replicated, switching to 'blind' dispersion method
then would heat treatment in time points be compared considering controls?
Thank you
cuffdiff doesn't really support very complicated designs. In your case it'll do pairwise comparisons between the samples (you don't have biological replicates?). If you need something more complicated then you'll need to use a different tool.