NAME

       cuffmerge - Merging assemblies

DESCRIPTION

       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.

SYNOPSIS

       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: 0.5 ]

       -p/--num-threads
              <int>            Use this many threads to merge assemblies.       [ default: 1 ]

       --keep-tmp
              Keep all intermediate files during merge