NAME

       cuffnorm - component of cufflinks suite

SYNOPSIS

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

DESCRIPTION

       cuffnorm v2.2.1 (Debian package) -----------------------------

              Supply  replicate  CXB  files  as  comma  separated  lists  for   each   condition:
              sample1_rep1.cxb,sample1_rep2.cxb,...sample1_repM.cxb

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

       -L/--labels
              comma-separated list of condition labels

       --norm-standards-file
              Housekeeping/spike genes to normalize libraries       [ default:   NULL ]

       -p/--num-threads
              number of threads used during quantification          [ default:      1 ]

       --library-type
              Library prep used for input reads                     [ default:  below ]

       --library-norm-method
              Method used to normalize library sizes                [ default:  below ]

       --output-format
              Format for output tables                              [ default:  below ]

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

       --total-hits-norm
              count all hits for normalization                      [ default:  FALSE ]

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

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

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

       --no-update-check
              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)