man cufflinks (1): component of cufflinks suite

SYNOPSIS

cufflinks [,options/] ,<hits.sam>/

cufflinks v2.2.1 linked against Boost version 105500 -----------------------------

-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 ]

-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 ]

-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 ]

--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 ]

-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 ]

: ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags