Category

Gene Expression Analysis


Usage

cuffnorm [options] <transcripts.gtf> <sample1_replicate1.sam[,…,sample1_replicateM.sam]> <sample2_replicate1.sam[,…,sample2_replicateM.sam]>… [sampleN.sam_replicate1.sam[,…,sample2_replicateM.sam]]


Manual

-h/–help
Prints the help message and exits
-o/–output-dir
Sets the name of the directory in which Cuffdiff will write all of its output. The default is “./”.
-L/–labels
Specify a label for each sample, which will be included in various output files produced by Cuffdiff.
-p/–num-threads
Use this many threads to align reads. The default is 1.
–total-hits-norm
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.
–compatible-hits-norm
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.
–library-type
–library-norm-method
–output-format
-v/–verbose
Print lots of status updates and other diagnostic information.
-q/–quiet
Suppress messages other than serious warnings and errors.
–no-update-check
Turns off the automatic routine that contacts the Cufflinks server to check for a more recent version.


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