Question: What is the purpose of Cufflink and Cuffmerge?
gravatar for k.ip
2.9 years ago by
k.ip10 wrote:

Hi guys,

I am new to the galaxy server, and I want to analyse my RNA-seq data with the following standard pipeline (TopHat=>Cufflinks=>Cuffmerge=>Cuffdiff) to determine differential expression between control and treatment group. However, both cufflink and cuffmerge only generate GTF file type but for Cuffdiff, they use BAM, so the only file i can use to run cuffdiff is the TopHat-generated files... But then what is the point to do Cufflinke and Cuffmerge exactly? Sorry guys, I am quite confused here.

Thanks in advance for answering my questions,




rna-seq cufflinks galaxy bam • 3.6k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by k.ip10
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Cufflinks 'assembles' mapped reads into transcripts defined by coordinates (no consensus is generated).

Cuffmerge 'merges' together these defined transcripts from Cufflinks along with a reference annotation GTF/GFF3 that also defines transcripts (iGenomes or similar). Only the transcripts in the reference annotation  GTF provided to Cuffdiff is considered during that tool's analysis. This can be Cuffmerge input or just the reference annotation GTF without using Cuffmerge - it depends on if discovery is part of the analysis.

More about the pipeline can be found at the author's web site and the Galaxy resources listed at the top of the Support wiki:

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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