cuffmerge [options]* <assembly_GTF_list.txt>
-h/–help
Prints the help message and exits
-o
Write the summary stats into the text output file
-g/–ref-gtf
An optional “reference” annotation GTF. The input assemblies are merged together with the reference GTF and included in the final output.
-p/–num-threads
Use this many threads to align reads. The default is 1.
-s/–ref-sequence
This argument should point to the genomic DNA sequences for the reference. If a directory, it should contain one fasta file per contig. If a multifasta file, all contigs should be present. The merge script will pass this option to cuffcompare, which will use the sequences to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats.