NAME

       cuffdiff - component of cufflinks suite

SYNOPSIS

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

DESCRIPTION

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

              Supply  replicate   SAMs   as   comma   separated   lists   for   each   condition:
              sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam

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

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

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

       -M/--mask-file
              ignore all alignment within transcripts in this file  [ default:   NULL ]

       -C/--contrast-file
              Perform the constrasts specified in this file         [ default:   NULL ]

       -b/--frag-bias-correct
              use bias correction - reference fasta required        [ default:   NULL ]

       -u/--multi-read-correct
              use 'rescue method' for multi-reads                   [ default:  FALSE ]

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

       --no-diff
              Don't generate differential analysis files            [ default:  FALSE ]

       --no-js-tests
              Don't perform isoform switching tests                 [ default:  FALSE ]

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

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

       --dispersion-method
              Method used to estimate dispersion models             [ default:  below ]

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

   Advanced Options:
       -m/--frag-len-mean
              average fragment length (unpaired reads only)         [ default:    200 ]

       -s/--frag-len-std-dev
              fragment length std deviation (unpaired reads only)   [ default:     80 ]

       -c/--min-alignment-count
              minimum number of alignments in a locus for testing   [ default:   10 ]

       --max-mle-iterations
              maximum iterations allowed for MLE calculation        [ default:   5000 ]

       --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 ]

       --emit-count-tables
              print count tables used to fit overdispersion         [    DEPRECATED   ]

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

       --num-frag-count-draws
              Number of fragment generation samples                 [ default:    100 ]

       --num-frag-assign-draws
              Number of fragment assignment samples per generation  [ default:     50 ]

       --max-frag-multihits
              Maximum number of alignments allowed per fragment     [ default: unlim  ]

       --min-outlier-p
              Min replicate p value to admit for testing            [    DEPRECATED   ]

       --min-reps-for-js-test
              Replicates needed for relative isoform shift testing  [ default:      3 ]

       --no-effective-length-correction
              No effective length correction                  [ default:  FALSE ]

       --no-length-correction
              No length correction                                  [ default:  FALSE ]

       -N/--upper-quartile-norm
              Deprecated, use --library-norm-method                 [    DEPRECATED   ]

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

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

       --poisson-dispersion
              Deprecated, use --dispersion-method                   [    DEPRECATED   ]

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

       --no-read-pairs
              Break all read pairs                                  [ default:  FALSE ]

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

       --no-scv-correction
              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