CUFFDIFF:(1)

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