Man page - cuffmerge(1)

Manual

CUFFMERGE

NAME
DESCRIPTION
Usage:
OPTIONS

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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

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