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Bioinformatics pipeline block to assemble transcriptome from aligned reads

Since R2023a

  • cufflinks block icon


A Cufflinks block enables you to assemble a transcriptome from aligned reads.

The block requires the Cufflinks Support Package for the Bioinformatics Toolbox™. If the support package is not installed, then a download link is provided. For details, see Bioinformatics Toolbox Software Support Packages.




b = bioinfo.pipeline.block.Cufflinks creates a Cufflinks block.

b = bioinfo.pipeline.block.Cufflinks(options) also specifies additional options.

b = bioinfo.pipeline.block.Cufflinks(Name=Value) specifies additional options as the property names and values of a CufflinksOptions object. This object is set as the value of the Options property of the block.

Input Arguments

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Cufflinks options, specified as a CufflinksOptions object, string, or character vector.

If you are specifying a string or character vector, it must be in the Cufflinks native syntax (prefixed by one or two dashes) [1].

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.


The following list of arguments is a partial list. For the complete list, refer to the properties of CufflinksOptions object.

Flag to normalize fragment counts to fragments per kilobase per million mapped reads (FPKM), specified as true or false.

Example: false

Data Types: logical

Additional commands, specified as a character vector or string.

The commands must be in the native syntax (prefixed by one or two dashes). Use this option to apply undocumented flags and flags without corresponding MATLAB® properties.

When the software converts the original flags to MATLAB properties, it stores any unrecognized flags in this property.

Example: '--library-type fr-secondstrand'

Data Types: char | string


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Function to handle errors from the run method of the block, specified as a function handle. The handle specifies the function to call if the run method encounters an error within a pipeline. For the pipeline to continue after a block fails, ErrorHandler must return a structure that is compatible with the output ports of the block. The error handling function is called with the following two inputs:

  • Structure with these fields:

    identifierIdentifier of the error that occurred
    messageText of the error message
    indexLinear index indicating which block process failed in the parallel run. By default, the index is 1 because there is only one run per block. For details on how block inputs can be split across different dimensions for multiple run calls, see Bioinformatics Pipeline SplitDimension.

  • Input structure passed to the run method when it fails

Data Types: function_handle

This property is read-only.

Input ports of the block, specified as a structure. The field names of the structure are the names of the block input ports, and the field values are bioinfo.pipeline.Input objects. These objects describe the input port behaviors. The input port names are the expected field names of the input structure that you pass to the block run method.

The Cufflinks block Inputs structure has the following field:

  • GenomicAlignmentFiles — Names of SAM or BAM files containing alignment records for each sample. This input is a required input that must be satisfied. The default value is a bioinfo.pipeline.datatypes.Unset object, which means that the input value is not set yet.

Data Types: struct

This property is read-only.

Output ports of the block, specified as a structure. The field names of the structure are the names of the block output ports, and the field values are bioinfo.pipeline.Output objects. These objects describe the output port behaviors. The field names of the output structure returned by the block run method are the same as the output port names.

The Cufflinks block Outputs structure has the following fields:

  • TranscriptsGTFFile — Transcript file name.

  • IsoformsFPKMFile — Estimated isoform-level expression file name.

  • GenesFPKMFile — Estimated gene-level expression file name.

  • SkippedTranscriptsGTFFile — Name of the file containing skipped transcripts when processing a locus.


To see the actual location of these files, first get the results of the block. Then use the unwrap method as shown in this example.

Data Types: struct

Cufflinks options, specified as a CufflinksOptions object. The default value is a default CufflinksOptions object.

Object Functions

compilePerform block-specific additional checks and validations
copyCopy array of handle objects
emptyInputsCreate input structure for use with run method
evalEvaluate block object
runRun block object


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Assemble a transcriptome using the provided SAM files which contain aligned reads from Mycoplasma pneumoniae from two samples.

import bioinfo.pipeline.block.*
import bioinfo.pipeline.Pipeline

samFiles = {which("Myco_1_1.sam"),which("Myco_1_2.sam")};
FC = FileChooser(samFiles);
CL = Cufflinks;

P = Pipeline;

R = results(P,CL)
R = 

  struct with fields:

           TranscriptsGTFFile: [1×2 bioinfo.pipeline.datatypes.File]
             IsoformsFPKMFile: [1×2 bioinfo.pipeline.datatypes.File]
                GenesFPKMFile: [1×2 bioinfo.pipeline.datatypes.File]
    SkippedTranscriptsGTFFile: [1×2 bioinfo.pipeline.datatypes.File]

Call unwrap on each field of the result structure R to see the location of each output file. For example, to see the location of TranscriptsGTFFile, enter the following.

ans = 

  2×1 string array



[1] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.

Version History

Introduced in R2023a