I've been running cuffdiff on some paired end rna seq samples with biological replicates. Before I started analyzing them I checked the dispersion plots using cummeRbund. For some reason it is forming a sharp cutoff which looks different from the examples on the websites. I have tried mapping both with tophat2.0.9 and STAR aligner and got identical results.
I have been using cuffdiff with the default options except for -b and using the genes.gtf file provided by the Illumina iGenomes download. Does anyone have ideas on what might be going wrong?
Thanks
I have been using cuffdiff with the default options except for -b and using the genes.gtf file provided by the Illumina iGenomes download. Does anyone have ideas on what might be going wrong?
Thanks
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