NAME

       cufflinks - component of cufflinks suite

SYNOPSIS

       cufflinks [options] <hits.sam>

DESCRIPTION

       cufflinks v2.2.1 linked against Boost version 108300 -----------------------------

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

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

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

       -G/--GTF
              quantitate against reference transcript annotations

       -g/--GTF-guide
              use reference transcript annotation to guide assembly

       -M/--mask-file
              ignore all alignment within transcripts in this file

       -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 ]

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

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

   Advanced Abundance Estimation 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 ]

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

       --compatible-hits-norm
              count hits compatible with reference RNAs only        [ default:  FALSE ]

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

       --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  ]

       --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   ]

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

   Advanced Assembly Options:
       -L/--label
              assembled transcripts have this ID prefix             [ default:   CUFF ]

       -F/--min-isoform-fraction
              suppress transcripts below this abundance level       [ default:   0.10 ]

       -j/--pre-mrna-fraction
              suppress intra-intronic transcripts below this level  [ default:   0.15 ]

       -I/--max-intron-length
              ignore alignments with gaps longer than this          [ default: 300000 ]

       -a/--junc-alpha
              alpha for junction binomial test filter               [ default:  0.001 ]

       -A/--small-anchor-fraction
              percent read overhang taken as 'suspiciously small'   [ default:   0.09 ]

       --min-frags-per-transfrag
              minimum number of fragments needed for new transfrags [ default:     10 ]

       --overhang-tolerance
              number of terminal exon bp to tolerate in introns     [ default:      8 ]

       --max-bundle-length
              maximum genomic length allowed for a given bundle     [ default:3500000 ]

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

       --min-intron-length
              minimum intron size allowed in genome                 [ default:     50 ]

       --trim-3-avgcov-thresh
              minimum avg coverage required to attempt 3' trimming  [ default:     10 ]

       --trim-3-dropoff-frac
              fraction of avg coverage below which to trim 3' end   [ default:    0.1 ]

       --max-multiread-fraction
              maximum fraction of allowed multireads per transcript [ default:   0.75 ]

       --overlap-radius
              maximum gap size to fill between transfrags (in bp)   [ default:     50 ]

   Advanced Reference Annotation Guided Assembly Options:
       --no-faux-reads
              disable tiling by faux reads                          [ default:  FALSE ]

       --3-overhang-tolerance
              overhang allowed on 3' end when merging with reference[ default:    600 ]

       --intron-overhang-tolerance
              overhang allowed inside reference intron when merging [ default:     30 ]

   Advanced Program Behavior Options:
       -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 ]

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

   Supported library normalization methods:
              classic-fpkm