Provided by: cufflinks_2.2.1+dfsg.1-3_amd64 bug


       cuffdiff - component of cufflinks suite


       cuffdiff    [options]   <transcripts.gtf>   <sample1_hits.sam>   <sample2_hits.sam>   [...


       cuffdiff v2.2.1 () -----------------------------

              Supply  replicate   SAMs   as   comma   separated   lists   for   each   condition:

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

              comma-separated list of condition labels

       --FDR  False discovery rate used in testing                  [ default:   0.05 ]

              ignore all alignment within transcripts in this file  [ default:   NULL ]

              Perform the constrasts specified in this file         [ default:   NULL ]

              use bias correction - reference fasta required        [ default:   NULL ]

              use 'rescue method' for multi-reads                   [ default:  FALSE ]

              number of threads used during quantification          [ default:      1 ]

              Don't generate differential analysis files            [ default:  FALSE ]

              Don't perform isoform switching tests                 [ default:  FALSE ]

              treat samples as a time-series                        [ default:  FALSE ]

              Library prep used for input reads                     [ default:  below ]

              Method used to estimate dispersion models             [ default:  below ]

              Method used to normalize library sizes                [ default:  below ]

   Advanced Options:
              average fragment length (unpaired reads only)         [ default:    200 ]

              fragment length std deviation (unpaired reads only)   [ default:     80 ]

              minimum number of alignments in a locus for testing   [ default:   10 ]

              maximum iterations allowed for MLE calculation        [ default:   5000 ]

              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 ]

              print count tables used to fit overdispersion         [    DEPRECATED   ]

              maximum fragments allowed in a bundle before skipping [ default: 500000 ]

              Number of fragment generation samples                 [ default:    100 ]

              Number of fragment assignment samples per generation  [ default:     50 ]

              Maximum number of alignments allowed per fragment     [ default: unlim  ]

              Min replicate p value to admit for testing            [    DEPRECATED   ]

              Replicates needed for relative isoform shift testing  [ default:      3 ]

              No effective length correction                  [ default:  FALSE ]

              No length correction                                  [ default:  FALSE ]

              Deprecated, use --library-norm-method                 [    DEPRECATED   ]

              Deprecated, use --library-norm-method                 [    DEPRECATED   ]

              Deprecated, use --library-norm-method                 [    DEPRECATED   ]

              Deprecated, use --dispersion-method                   [    DEPRECATED   ]

   Debugging use only:
              Skip a random subset of reads this size               [ default:    0.0 ]

              Break all read pairs                                  [ default:  FALSE ]

              Trim reads to be this long (keep 5' end)              [ default:   none ]

              Disable SCV correction                                [ default:  FALSE ]

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

   Supported dispersion methods:
              blind per-condition poisson pooled (default)

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