It produces a number of output files that contain expression levels and normalized fragment counts at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene.
cuffnorm [options] <transcripts.gtf> <sample1_replicate1.sam[,â€¦,sample1_replicateM.sam]> <sample2_replicate1.sam[,â€¦,sample2_replicateM.sam]>â€¦ [sampleN.sam_replicate1.sam[,â€¦,sample2_replicateM.sam]]
Prints the help message and exits
Sets the name of the directory in which Cuffdiff will write all of its output. The default is “./”.
Specify a label for each sample, which will be included in various output files produced by Cuffdiff.
Use this many threads to align reads. The default is 1.
With this option, Cuffquant counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. It is inactive by default.
With this option, Cuffnorm counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. It is active by default.
Print lots of status updates and other diagnostic information.
Suppress messages other than serious warnings and errors.
Turns off the automatic routine that contacts the Cufflinks server to check for a more recent version.