Hello. I ran Cuffdiff on some RNAseq data last weekend, and it completed in about 48 hours. However, I discovered that I didn’t select the option to generate the SQLite file for use in CummeRbund. So, I re-ran the same analysis, but it’s been running for four days now. I have two questions:
- Should it take this long to run?
- How consistent are Cuffdiff’s outputs between runs? Will genes that came up as differentially expressed from the first time I ran Cuffdiff have the same results the second time around (ie does Cuffdiff use any random error to generate its results)? Or do I need to wait for it to finish re-running to start my follow-up analysis?