Class: Bio::Ngs::Cufflinks::Quantification
- Inherits:
-
Object
- Object
- Bio::Ngs::Cufflinks::Quantification
- Includes:
- Command::Wrapper, Utils
- Defined in:
- lib/bio/appl/ngs/cufflinks.rb
Overview
cufflinks v1.3.0 linked against Boost version 104000
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 ]
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 ]
--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 ]
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
Direct Known Subclasses
Method Summary
Methods included from Utils
Methods included from Command::Wrapper
#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?