cuffmerge - 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>
- -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