CUFFMERGE(1)

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