Class: Bio::Ngs::Cufflinks::GffRead

Inherits:

Object

Object
Bio::Ngs::Cufflinks::GffRead

show all

Includes:: Command::Wrapper

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

Overview

-E expose (warn about) duplicate transcript IDs and other potential

    problems with the given GFF/GTF records
-Z  merge close exons into a single exon (for intron size<4)
-w  write a fasta file with spliced exons for each GFF transcript
-x  write a fasta file with spliced CDS for each GFF transcript
-W  for -w and -x options, also write for each fasta record the exon
    coordinates projected onto the spliced sequence
-y  write a protein fasta file with the translation of CDS for each record
-L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
-m  <chr_replace> is a reference (genomic) sequence replacement table with
    this format:
    <original_ref_ID> <new_ref_ID>
    GFF records on reference sequences that are not found among the
    <original_ref_ID> entries in this file will be filtered out
-o  the "filtered" GFF records will be written to <outfile.gff>
    (use -o- for printing to stdout)
-t  use <trackname> in the second column of each GFF output line
-T  -o option will output GTF format instead of GFF3

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?