Page tree
Skip to end of metadata
Go to start of metadata

Cuffdiff takes a transcript file as input, along with two or more fragment alignments (e.g. in SAM format) for two or more samples. It produces a number of output files that contain test results for changes in expression at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene.

Element type: cuffdiff


ParameterDescriptionDefault valueParameter in Workflow FileType
Output directoryDirectory to save MACS output files.


Time series analysisIf set to True, instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order.Falsetime-series-analysisboolean
Upper quartile normIf set to True, normalizes by the upper quartile of the number of fragments mapping to individual loci instead of the total number of sequenced fragments. This can improve robustness of differential expression calls for less abundant genes and transcripts.False upper-quartile-normboolean
Hits norm Instructs how to count all fragments. Total specifies to count all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible specifies to use only compatible fragments. Selecting Compatible is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes..Compatiblehits-normnumeric
Frag bias correctProviding the sequences your reads were mapped to instructs Cuffdiff to run bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates..
Multi read correctDo an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.Falsemulti-read-correctboolean
Library typeSpecifies RNA-Seq protocol.Standard Illuminalibrary-typenumeric
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..
Min alignment countThe minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing..10 min-alignment-countstring
FDRThe allowed false discovery rate used in testing.0.05 fdrnumeric
Max MLE iterationsSets the number of iterations allowed during maximum likelihood estimation of abundances.5000max-mle-iterationsnumeric
Emit count tablesInclude information about the fragment counts, fragment count variances, and fitted variance model into the report.Falseemit-count-tablesboolean
Cuffdiff tool pathThe path to the Cuffdiff external tool in UGENE.defaulpathstring
Temporary directoryThe directory for temporary files.defaulttemp-dirstring

Input/Output Ports

The element has 2 input port:

Name in GUI: Annotations

Name in Workflow File: in-annotations


Slot In GUISlot in Workflow FileType
Set of annotationsin-annotationsann_table

Name in GUI: Assembly

Name in Workflow File: in-assembly


Slot In GUISlot in Workflow FileType
Assembly dataassemblyassembly
Source urlurlstring
  • No labels