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

Parameters in GUI

ParameterDescriptionDefault value
Output directoryDirectory to save MACS output files. 
Reference annotationTells Cufflinks to use the supplied reference annotation to estimate isoform expression. Cufflinks will not assemble novel transcripts and the program will ignore alignments not structurally compatible with any reference transcript. 
RABT annotationTells Cufflinks to use the supplied reference annotation to guide Reference Annotation Based Transcript (RABT) assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled. 
Library typeSpecifies RNA-Seq protocol.Standart Illumina
Mask fileIgnore all reads that could have come from transcripts in this file. It is recommended to include any annotated rRNA, mitochondrial transcripts other abundant transcripts you wish to ignore in your analysis in this file. Due to variable efficiency of mRNA enrichment methods and rRNA depletion kits, masking these transcripts often improves the overall robustness of transcript abundance estimates. 
Multi-read correctTells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.False
Min isoform fractionAfter calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them.0.1
Frag bias correctProviding Cufflinks with a multifasta file via this option instructs it to run the bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates. 
Pre-mRNA fractionSome RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored.0.15
Cufflinks tool pathThe path to the Cufflinks external tool in UGENE.default
Temporary directoryThe directory for temporary files.default

Parameters in Workflow File

Type: cufflinks

ParameterParameter in the GUIType
out-dirOutput directory


ref-annotationReference annotationstring
rabt-annotationRABT annotationstring
library-typeLibrary typenumeric
mask-fileMask filestring
multi-read-correctMulti-read correctboolean
min-isoform-fractionMin isoform fractionnumeric
frag-bias-correctFrag bias correctstring
pre-mrna-fractionPre-mRNA fractionnumeric
pathCufflinks tool pathstring
tmp-dirTemporary directorystring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input reads

Name in Workflow File: in-assembly


Slot In GUISlot in Workflow FileType
Assembly dataassemblyassembly
Source urlurlstring

And 1 output port:

Name in GUI: Output annotations

Name in Workflow File: out-annotations


Slot In GUISlot in Workflow FileType
Isoform-level expression valuesisolevel.slotann_table
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