Provided by: cufflinks_1.3.0-1ubuntu2_amd64 bug

NAME

       cufflinks  - Transcript assembly, differential expression, and differential regulation for
       RNA-Seq

DESCRIPTION

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

SYNOPSIS

       cufflinks [options] <hits.sam>

OPTIONS

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

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

       -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 ]

   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 ]

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

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

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

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

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

   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 ]

       --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 ]

   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

       cufflinks  v1.0.2 linked against Boost version 104601 ----------------------------- Usage:
       cufflinks [options] <hits.sam> General Options:

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

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

       -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 ]

   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 ]

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

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

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

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

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

   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 ]

       --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 ]

   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