NAME

       cuffmerge - component of cufflinks suite

DESCRIPTION

       cuffmerge:  cuffmerge  takes two or more Cufflinks GTF files and merges them into a single
       unified transcript catalog.  Optionally, you can provide the script with a reference  GTF,
       and the script will use it to attach gene names and other metadata to the merged catalog.

   Usage:
              cuffmerge [Options] <assembly_GTF_list.txt>

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