I wanted to do differential gene expression testing using RNA-seq data.I have 4 groups. 1 control and 3 diseased.
In each group I have 3 or 4 samples.
G1-4 samples (Control)
G2- 4 Samples (Disease 1)
G3- 3 Samples (Disease 2)
G4- 4 Samples (Disease 3)
In cuffdiff, I have uploaded the combined transcript file from cuffcompare.
Then for the conditions, I have 15 BAM files for 15 samples. In each condition I uploaded each sample (so total no. of conditions would be 15).
I am getting the following error.
Fatal error: Exit code 134 () [03:39:08] Loading reference annotation and sequence. Warning: No conditions are replicated, switching to 'blind' dispersion method [03:39:31] Inspecting maps and determining fragment length distributions. [04:02:57] Modeling fragment count overdispersion.
Actually I wanted to download the gene FPKM tracking file from cuffdiff and do the differential gene expression analysis using BRB array tools.
Please help how to solve this.