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cuffmerge - component of cufflinks suite

CUFFMERGE(1) User Commands CUFFMERGE(1)

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
November 2017 cuffmerge 2.2.1+dfsg.1-2