Provided by: cufflinks_2.2.1+dfsg.1-2_amd64 bug


       cuffnorm - component of cufflinks suite


       cuffnorm    [options]   <transcripts.gtf>   <sample1_expr.cxb>   <sample2_expr.cxb>   [...


       cuffnorm v2.2.1 () -----------------------------

              Supply  replicate  CXB  files  as  comma  separated  lists  for   each   condition:

   General Options:
              write all output files to this directory              [ default:     ./ ]

              comma-separated list of condition labels

              Housekeeping/spike genes to normalize libraries       [ default:   NULL ]

              number of threads used during quantification          [ default:      1 ]

              Library prep used for input reads                     [ default:  below ]

              Method used to normalize library sizes                [ default:  below ]

              Format for output tables                              [ default:  below ]

   Advanced Options:
              count hits compatible with reference RNAs only        [ default:   TRUE ]

              count all hits for normalization                      [ default:  FALSE ]

              log-friendly verbose processing (no progress bar)     [ default:  FALSE ]

              log-friendly quiet processing (no progress bar)       [ default:  FALSE ]

       --seed value of random number generator seed                 [ default:      0 ]

              do not contact server to check for update availability[ default:  FALSE ]

   Supported library types:
              ff-firststrand   ff-secondstrand   ff-unstranded   fr-firststrand   fr-secondstrand
              fr-unstranded (default) transfrags

   Supported library normalization methods:
              classic-fpkm geometric (default) geometric quartile

   Supported output formats:
              cuffdiff simple-table (default)