cufflinks
- Version:
2.2.1
- Category:
bio
- Cluster:
Loki
Description
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Documentation
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
Examples/Usage
List available modules:
$ module avail cufflinks
Load the cufflinks module:
$ module load bio/cufflinks/2.2.1
Check the loaded modules:
$ module list
Unload the cufflinks module:
$ module unload bio/cufflinks/2.2.1
Installation
Source code is obtained from Cufflinks