cuffmerge(1) component of cufflinks suite


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.


cuffmerge [Options] <assembly_GTF_list.txt>


Prints the help message and exits
<output_dir> Directory where merged assembly will be written [ default: ./merged_asm ]
An optional "reference" annotation GTF.
<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 ]
<int> Use this many threads to merge assemblies. [ default: 1 ]
Keep all intermediate files during merge