Provided by: cufflinks_2.2.1+dfsg.1-2_amd64 
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