[BioC] Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks

[Nicolas Delhomme]

Hi Rich,

Yes it can, just use the "gtf" as the annotationMethod argument. Note that I expect the gtf file to be formatted according to that description: http://genome.ucsc.edu/FAQ/FAQformat.html#format4. There's more details about this in the easyRNASeq vignette. I haven't had any problems using the cuffmerge/cuffcompare gtfs, but it's always worth a check.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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On Dec 4, 2012, at 4:54 PM, Richard Friedman wrote:

> 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)
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> http://cancercenter.columbia.edu/~friedman/
> 
> In memoriam, Ray Bradbury
> 
>