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Cufflinks includes a script called cuffmerge that you can use to merge together several Cufflinks assemblies. It handles also handles running Cuffcompare for you, and automatically filters a number of transfrags that are probably artfifacts. If you have a reference GTF file available, you can provide it to the script in order to gracefully merge novel isoforms and known isoforms and maximize overall assembly quality. The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff.

Version 1.0
Bundle sequencing
Specialties generic
Authors Alejandra Cervera (alejandra.cerverataboada@helsinki.fi)
Issue tracker View/Report issues
Requires Cufflinks ; installer (bash)
Source files component.xml Cuffmerge.java
Usage Example with default values

This component is not being used anymore, last update to the software was 4 years ago.

Type parameters (generics)


Name Type Mandatory Description
arrayIn Array<BinaryFile> Mandatory Text file "manifest" with a list (one per line) of GTF files that you'd like to merge together into a single GTF file.
ref_gtf GTF Optional An optional "reference" annotation GTF. The input assemblies are merged together with the reference GTF and included in the final output.
ref_seq SequenceSet Optional 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. Note that seq_dir must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.


Name Type Description
merged GTF Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.


Name Type Default Description
help boolean false Prints the help message and exits.
num_threads int -1 Use this many threads to align reads. The default is 1.

Test cases

Test case Parameters IN
case1 properties arrayIn ref_gtf ref_seq (missing)

# Testing cufflinks component

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