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Richard Friedman
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@richard-friedman-513
Last seen 10.2 years ago
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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