I performed Cuffdiff between two samples with three replicates each. While gene_exp.diff, cds_exp.diff and splicing.diff files are filled with entries, promoter.diff and isoform_exp.diff files are empty. This is a bit unusual. Here is the command for cuffdiff
cuffdiff --use-sample-sheet -C contrasts.txt -p 10 -o ../cuffdiff ../cuffmerge/merged.gtf sample_sheet.txt
merged.gtf was produced using following command
cuffmerge -o ../cuffmerge/ -g annotation.gtf -s assembly.genome.fa -p 10 assembly_GTF_list.txt
This happened to two consecutive datasets. I am thinking of reinstalling Cufflinks. Any other suggestions?