Class: Bio::Ngs::Cufflinks::Merge

Inherits:

Object

Object
Bio::Ngs::Cufflinks::Merge

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Includes:: Command::Wrapper

Defined in:: lib/bio/appl/ngs/cufflinks.rb

Overview

Options:

-h/--help                               Prints the help message and exits
-o                     <output_dir>     Directory where merged assembly will be written  [ default: ./merged_asm  ]
-g/--ref-gtf                            An optional "reference" annotation GTF.
-s/--ref-sequence      <seq_dir>/<seq_fasta> Genomic DNA sequences for the reference.
--min-isoform-fraction <0-1.0>          Discard isoforms with abundance below this       [ default:           0.05 ]
-p/--num-threads       <int>            Use this many threads to merge assemblies.       [ default:             1  ]
--keep-tmp                              Keep all intermediate files during merge

Method Summary

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?