Question: GFF model in Tophat and/or Cufflinks?
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gravatar for manekineko
5.3 years ago by
manekineko130
manekineko130 wrote:

Does it makes difference if I provide GFF only to Cuflinks (after the Tophat mapping) or when I provide it to both Tophat and than again to Cufflinks?

rna-seq • 1.3k views
ADD COMMENTlink modified 5.3 years ago by Manvendra Singh2.1k • written 5.3 years ago by manekineko130
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gravatar for Manvendra Singh
5.3 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

In TopHat, if you provide GFF, then it would make transcriptome sequence out of it , and maps entire read on it. But at end of the day, it maps segmental reads to the reference genome, so GFF is for guiding the assembly.

I work with junctions so I always go for tophat without providing GFF/GTF then I go for RABT assembly from Cufflinks and then I provide resultant gtf to tophat2 to reassemble.

I see that providing GFF to tophat would improve the quality of mapping.

ADD COMMENTlink written 5.3 years ago by Manvendra Singh2.1k
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