Cufflinks protocols

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Cufflinks computational protocol

Cufflinks specifications

Information


Unique identifier OMICS_01304
Name Cufflinks
Software type Application/Script
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
Programming languages C++
Computer skills Advanced
Version 2.2.1
Stability Stable
Maintained Yes

Subtools


  • Cuffcompare
  • Cuffdiff
  • Cuffmerge
  • Cuffnorm
  • Cuffquant

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Versioning


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Documentation


Maintainers


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

Publications for Cufflinks

Cufflinks IN pipelines

 (1225)
2018
PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] rna-seq data was aligned to the human genome hg19 using tophat. unmapped reads were filtered out. transcripts were assembled by cufflink. differential expression of transcripts was estimated by cuffdiff 9. for chip-seq data, bowtie2 was used for mapping the chip-seq data to the human genome hg19. data from repeated experiments were merged for analysis. unmapped reads were filtered out. […]

2018
PMCID: 5751775
PMID: 29298675
DOI: 10.1186/s12870-017-1218-9

[…] trimmed by using btrim [42]. reads were aligned to the reference genome of btx623 (sbicolor_v1.4_79) [43] by using tophat version 2.0.4 [44]. differentially expressed genes were identified by using cuffdiff version 2.2.0 [45], with the gene models annotated in sbicolor ver1.4 [46]., mapman (3.5.1 r2) software [47] was used to map the ratio of expression (lodged to intact) of each gene to known […]

2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] abundance of transcripts were determined by mapping quality-filtered and adapter-trimmed reads (trimmomatic v0.36) to the published reference genome of g. oxydans using bowtie2 v2.2.7 [41, 42]. cufflinks and cuffnorm were used to quantify transcript levels [43]., detection of tsss was done with libraries enriched for primary transcripts using readxplorer [44] with the following parameters: […]

2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] of transcripts were determined by mapping quality-filtered and adapter-trimmed reads (trimmomatic v0.36) to the published reference genome of g. oxydans using bowtie2 v2.2.7 [41, 42]. cufflinks and cuffnorm were used to quantify transcript levels [43]., detection of tsss was done with libraries enriched for primary transcripts using readxplorer [44] with the following parameters: (i) […]

2018
PMCID: 5758603
PMID: 29354153
DOI: 10.3389/fpls.2017.02226

[…] paired reads were then mapped to the arabidopsis genome using tophat. the fragment alignments generated by tophat were then used as input files to be further analyzed through the recommended cufflinks packages to detect the differentially expressed genes between wt and 35s:mir156 arabidopsis plants., plant tissues were collected at specific time points as indicated in results for gene […]

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.

Cufflinks reviews

 (2)
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Sangram keshari sahu

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When it comes to post-mapping, Cufflinks-tools along with its sub modules (Cuffmerge, Cuffdiff) is good for transcriptome assembly and differential expression analysis (DEG) with RNA-Seq datasets. Because it handles the normalization internally, without additional steps. Being one of the oldest pipelines, there are several supporting tools developed for publication ready visualizations (Ex: CummeRbund). Although a similar tool "StringTie (faster to Cufflinks Assembler)" available, they still use some modules like CuffDiff to do DEG analysis.

Arup Ghosh

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Cufflinks is one of the earliest tools for differential gene expression analysis tools with FPKM/RPKM normalization. This tool is also capable of carrying out isoform abundance quantification and differential expression.