On Dec 4, 2012, at 5:27 AM, Nicolas Delhomme wrote:
> 
> 
> As I said, I have a very similar setup, but completely de-novo. I've been (still am) testing several approaches:
> 
> 1) running TopHat/Cufflinks/Cuffmerge (cuffmerge to get the exon/gene GFF) and from that I go back to the original alignments by tophat and use these as input together with the GFF for easyRNASeq. I then get my DESeq/edgeR output and proceed in R.

Nico,

	Thanks for your definitive and quick reply. I have a question on your option 1.
Cufflinks/Cuffmerge ouputs a GTF file. Can the GTF file be used instead of a GFF file in
easyRNASeq? I know that the GTF format  files are extensions of the GFF format  files but 
can GTF be used in place of GFF  in easyRNASeq?

Thanks and best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)/
Columbia Initiative in Systems Biology
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
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friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Ray Bradbury

	
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