NAME

       cuffdiff - find significant changes in transcript expression, splicing, and promoter use

SYNOPSIS

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

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

DESCRIPTION

       see online page http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

OPTIONS

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

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

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

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

       -M/--mask-file
              ignore all alignment within transcripts 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 (more accurate)   [ default:  FALSE ]

       -N/--upper-quartile-norm
              use upper-quartile normalization                      [ default:  FALSE ]

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

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

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

       -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 ]

       --num-importance-samples
              number of importance samples for MAP restimation      [ default:   1000 ]

       --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 ]

       --poisson-dispersion
              Don't fit fragment counts for overdispersion          [ default:  FALSE ]

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

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

       --no-update-check
              do not contact server to check for update availability[ default:  FALSE ]

       --emit-count-tables
              print count tables used to fit overdispersion         [ default:  FALSE ]

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