HPC:cufflinks

Cufflinks

Cufflinks version 2.2.0 is installed across all HPC nodes

Usage/default output

Cufflinks is made available via a module file:

[asrini@node061 ~]$ module load cufflinks-2.2.0

[asrini@node061 ~]$ which cufflinks
/opt/software/cufflinks/2.2.0/bin/cufflinks

[asrini@node061 ~]$ cufflinks
cufflinks v2.2.0
linked against Boost version 104700
-----------------------------
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 ]
  --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

Other Pages

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• HPC FAQ
• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System