Hello everybody, I'm very new in RNA seq analysis I have run cuffdiff on 3 condition dataset collections( each collection has 4 replicates) using GALAXY with the cufmerg GTF file, but I got an error, I have repeated the same job many and many times, unfortunately, got the same result. I couldn't understand what that report means and what I have to change. Fatal error: [20:15:32] Loading reference annotation. [20:15:33] Inspecting maps and determining fragment length distributions. [20:36:35] Modeling fragment count overdispersion. [20:38:50] Modeling fragment count overdispersion. [20:41:08] Modeling fragment count overdispersion.
Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3495302.83 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.52 Estimated Std Dev: 44.72 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3383043.21 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.51 Estimated Std Dev: 44.06 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3904499.36 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.72 Estimated Std Dev: 45.10
does that relate to that I have the problem with my mapping process so need to realighn my data again? update I have rune cuffdiff without Generate SQLite, got the same problem I have run cuffdiff with the reference annotation file downloaded from iGenom instead of cufmerge GTF, I wasn't lucky
My question so far, what that error means?
because the error includes Map Properties does that mean I have a problem with my alignment process?
Estimated Mean 202. does that mean I need a double check to the inner distance of the paired-end read?
really I'm confused now and stuck on this step days ago with no productive progress,
any suggestion or explanation of that error will help me and will be fully appreciated
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