Cufflinks specifications


Unique identifier OMICS_01304
Name Cufflinks
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format GTF, GFF, SAM, BAM, FASTA, TSV, CXB, FPKM_tracking
Output format GTF, GFF, SAM, BAM, FASTA, TSV, CXB, FPKM_tracking, DIFF
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • Cuffdiff
  • Cuffnorm
  • Cuffquant
  • Cuffmerge
  • Cuffcompare



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  • person_outline Lior Pachter <>
  • person_outline Cole Trapnell <>

Cufflinks articles

Cufflinks citations

PMCID: 5937014

[…] trimmomatic (trapnell and schatz, 2009). clean reads were mapped to the mouse reference genome (mm10) using tophat followed by transcript assembly and differential gene expression analysis using cufflinks. the expression of every gene was measured by fpkm (fragments per kilobase of transcript per million fragments mapped). genes and transcripts were annotated using gene transcription […]

PMCID: 5916904

[…] using cufflinks v2.2.173. fragments per kilobase of exon per million fragments mapped (fpkm) were used to normalize rna-seq fragment counts and estimate the relative abundance of each gene. the cuffdiff package in cufflinks was used to perform pairwise comparisons of the expressions of each gene between treatments and control in the four species and to report degs and transcripts. the degs […]

PMCID: 5917015

[…] and aligned with hisat2 (kim et al., 2015) against the same z. mays reference genome as was used for rrbs. alignment was done mainly with options and the additional options –phred64, –dta-cufflinks, –no-mixed, and –no-discordant. transcript assembling was done via cufflinks from the cufflinks suite of tools (trapnell et al., 2010) with the –gtf-guide (using the same annotation files […]

PMCID: 5906695

[…] rna-seq reads (2 × 101 bp) were aligned to the human genome (hg19) using tophat2-2.0.12 (default parameter and—library-type fr-firststrand). transcript abundances at the gene level were estimated by cufflinks70. the normalized counts of rna sequencing data of 35 tumors from the tcga cohort were obtained from the genomic data commons portal., the somatic mutation rate is correlated […]

PMCID: 5895821

[…] the reads with high mapping quality (mapq ≥ 20) were used for further analyses. the expression level of each gene was calculated as reads per kilobase per million mapped reads (rpkm) by cufflinks-2.2.169 and analyzed using genespring software. genes whose rpkm was > 2 in all samples were included. genes expressed in control npcs on the 0.5-kpa matrix more than 2-fold compared […]

Cufflinks institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Computer Science, University of California, Berkeley, CA, USA; Computer Science and Artificial Intelligence Lab, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Mathematics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
Cufflinks funding source(s)
Supported by US National Institutes of Health grants R01-HG006102 and R01-HG006129-01, Damon Runyon Cancer Foundation Fellow, National Science Foundation Postdoctoral Fellow, National Science Foundation Graduate Research Fellow, Damon Runyon-Rachleff, Searle, and Smith Family Scholar, and is supported by Director's New Innovator Awards (1DP2OD00667-01) and the Center of Excellence in Genome Science from the US National Human Genome Research Institute.

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