I am dealing with a bacterium which has about 4000 genes. When I tried Cuffmerge to merge everything with reference annotation, I got a merged file of only 50 lines. If I left out the reference annotation file, Cuffmerge returned me a merged file of 4000 lines (which is more reasonable).
However this difference didn't happen if I use Cuffcompare to merge all the files. With or Without reference annotation, the merged file are both of 4000 lines. If I continue to Cuffdiff with this Cuffcompare file, I got over 1000 significantly changed genes.
Could you give me some suggestion on this? Should I just trust the Cuffcompare file?
Cuffmerge attempts to remove incomplete or spurious transcripts. My best guess is bacterial transcripts, with few/no introns, are being filtered out because they appear to be incomplete to Cuffmerge. So, in your case, Cuffcompare could be the superior option.
You might want to verify my guess by discussing the issue with the cufflinks developers directly: tophat.cufflinks@gmail.com ; please feel free to post anything you learn to this list.
Best, J.