Assembly Transcripts with Cufflinks Element

Cufflinks accepts aligned RNA-Seq reads and assembles these alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on the number of reads supporting each one, taking into account biases in library preparation protocols.

Element type: cufflinks

Parameters

Parameter	Description	Default value	Parameter in Workflow File	Type
Output directory	Directory to save MACS output files.		out-dir	string
Reference annotation	Use the supplied reference annotation to estimate isoform expression. Novel transcripts will not be assembled. Alignments not compatible with any reference transcript are ignored.		ref-annotation	string
RABT annotation	Use the supplied reference annotation to guide Reference Annotation Based Transcript (RABT) assembly. Adds faux reads. Output includes reference transcripts and any novel transcripts.		rabt-annotation	string
Library type	Specifies RNA-Seq protocol.	Standard Illumina	library-type	numeric
Mask file	Reads from transcripts in this file are ignored (e.g., rRNA, mitochondrial). Masking improves the robustness of abundance estimates.		mask-file	string
Multi-read correct	Enable procedure to better weight reads mapping to multiple genome locations.	False	multi-read-correct	boolean
Min isoform fraction	Filters out very low abundance transcripts that may be unreliable or artifacts. Also filters introns with few supporting alignments.	0.1	min-isoform-fraction	numeric
Frag bias correct	Run bias correction algorithm using the provided multi-FASTA file of the genome. Improves abundance estimates.		frag-bias-correct	string
Pre-mRNA fraction	Filters intronic alignments if they are likely pre-mRNA. The value defines the threshold for intron depth vs. splice reads.	0.15	pre-mrna-fraction	numeric
Cufflinks tool path	Path to the Cufflinks external tool in UGENE.	default	path	string
Temporary directory	Directory for temporary files.	default	tmp-dir	string

Input/Output Ports

The element has 1 input port:

Name in GUI: Input reads
Name in Workflow File: in-assembly
Slots:

Slot In GUI	Slot in Workflow File	Type
Assembly data	assembly	assembly
Source url	url	string

And 1 output port:

Name in GUI: Output annotations
Name in Workflow File: out-annotations
Slots:

Slot In GUI	Slot in Workflow File	Type
Isoform-level expression values	isolevel.slot	ann_table