Dear Bioconductor List,

	I am working through the  easyRNAseq use case to learn how 
to obtain counts in RNASeq experiments for further analysis.
The example starts with BAM files and converts BAM files to Exons,
transcripts and genes using geneModels. 

Does using geneModels only assemble previously annotated transcripts and
genes OR can it find new ones if present?

If it can find new ones how well does it do this in comparison to Cufflinks?

If it cannot find new ones - is there a way to get counts (as distinct from fpkm
values) for genes and transcripts from  cufflinks and 
relate them to existing annotation where they correspond and present them
as non-previosuly annotated ones when they don't correspond?

Can easyRNASeq be used for this purpose?
Can anyone recommend a tool that can be used for this purpose?

My goal is to get a set of counts that can be input into CQN and then edgeR.
I wish to use TopHat/Cufflinks to get the Exons, transcripts, and genes including
novel spliced variants but I am persuaded CQN is a better way to normalize than
FPKM and edgeR is a better way to analyze differential expression than 
Cuffdiff. 

I would appreciate any advice.

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
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Ray Bradbury


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