[BioC] easyRNAseq question

Akula, Nirmala (NIH/NIMH) [C] akulan at mail.nih.gov
Fri May 25 23:07:21 CEST 2012

Dear Nico,

Thank you very much for your response. I did read the sections that you mentioned but would like to know more details about the BestExon method. Here is what I currently have:

1. Map reads with TopHat
2. Create a bed file from the bam (each read is represented by only one base which is its starting position to make sure that the read does not fall on two different exons)
3. Use coverageBed to get the counts reads on each exon
4. For gene-level differential expression: Take only one exon/gene that has the maximum number of reads
5. Analyze the reads in DESeq

I would like to compare the above method to the BestExon method in easyRNAseq.


-----Original Message-----
From: Nicolas Delhomme [mailto:delhomme at embl.de] 
Sent: Friday, May 25, 2012 3:03 AM
To: Akula, Nirmala (NIH/NIMH) [C]
Cc: bioconductor at r-project.org
Subject: Re: easyRNAseq question

Dear Nirmala,

I've Cc'ed your email to the Bioconductor mailing list, as it might help other users.

Yes, there is currently a manuscript in review. 

As I'm not sure where you got your information from about the GeneModel summarization, I would direct you to read the new vignette of the development package: http://bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html, page 10 and section 4.6. If that's what you've done or if the information there is not sufficient, let me know and I'll detail it more. By the way, the BestExon summarization did not really prove useful on the datasets I've been working on. I'm thinking about deprecating it.



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

On May 24, 2012, at 11:46 PM, Akula, Nirmala (NIH/NIMH) [C] wrote:

> Dear Nicolas,
> Is there a publication that is available for easyRNAseq software? Also, you have mentioned that the transcripts are collapsed to genes by BestExon method and GeneModel summarization. Could you give details on these two methods?
> Thank you very much.
> Best Regards,
> Nirmala

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