Provided by: cufflinks_2.1.1-4_amd64
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