I'm trying to run cuffdiff as part of an RNA-seq project, and it's not working. I've tried leaving it to run overnight 3 times now and every time it starts the job but ends up giving me a tool error for all the files it's trying to create.
I'm using a cuffmerge assembly in my transcript input. Here are other specifications:
- Omit tabular datasets: No
- Generate SQlite: Yes
- Input: BAM files from alignments I did with TopHat (for each, 2 technical replicates were merged with BAM Tools). There are 3 conditions and 6 biological replicates in each.
- Library normalization method: Quartile
- Dispersion estimation method: pooled
- False discovery rate: 0.05
- Min alignment count: 10
- Use multi-read correct: Yes
- Perform bias correction: Yes, "Locally cached", "Mouse (Mus Musculus): mm10"
- Include read group datasets: No
- Include count based output files: No
- Apply length correction: Cufflinks effective length correction
- Set additional parameters for single end reads: No
- Set advanced cuffdiff parameters: No
- Job resource parameters: Use default job resource parameters
Any help would be greatly appreciated.