I found in the output of cuffnorm there was no locus information corresponding to my de novo assembly, whereas in the output of cuffdiff, there was a column telling the loci of differentially expressed genes so that I can map the loci with the BLAST output.
The reason I did both was because in cuffdiff output there was no count for a certain gene in a replicate. I found the tracking ID in cuffnorm output looked like the test ID in cuffdiff. Are they the same? If so, I can extract the differentially expressed gene from cuffdiff then filter the table of cuffnorm. Otherwise, how could I use the tracking ID in cuffnorm?