So I think I have found an odd bug for cufflinks, that I can not find any mention of it in any blogs online.
For output while running cufflinks, sometimes I received a "transcripts.gtf" file and sometimes I do not. Same gtf input files and options for cufflinks are used. I have repeated it twice now with the same results. The only difference is a different bam file.
cufflinks -p [number of threads to use] -g [path to Rat gtf file] -o [path for output directory] [.bam file]
Performing RNA-Seq analysis on several hundred rat samples in order to provide an expression profile. I have run tophat 2.0 to align fasta files to the current rat genome to generate the .bam files. Using cufflinks 2.2 to generate the transcripts.gtf in order to make a new gtf reference file to merge downstream with cuffmerge in order to perform cuffdiff analysis. This protocol has been recommended by trapnell et al and I have successfully run the protocol using human, rat (different), mouse, and dog data. This is the first time I have come across this problem.
Any suggestions or possible solutions?