Bomba,

I'm not familiar enough with bacterial/prokaryotic transcriptomes to suggest a 
possible workflow. You might try the standard 
Tophat-Cufflinks-Cuffcompare/merge-Cuffdiff workflow and see whether you get 
meaningful results; Tophat runs Bowtie internally, so there's no reason to run 
Bowtie separately unless there are Bowtie-specific parameters that you need to 
modify. I've had very little experience with PALMapper and can't speak to its 
efficacy, either for eukaryotic or prokaryotic transcriptome analyses.

Finally, I've cc'd the galaxy-user mailing list. Using this list is the best 
way to reach the Galaxy user community and get in touch with someone that has 
used Galaxy to analyze bacterial transcriptomes.

Good luck,
J.


On Feb 16, 2012, at 9:17 AM, Bomba Dam wrote:

> Dear Dr. Goecks,
> 
> I am working as a post-doctoral fellow in MPI Marburg, Germany. We am trying 
> to understand the differential expression of genes in a methanotrophic 
> bacterium under different growth conditions. We are sequencing the 
> transcriptome using Illumina Hiseq. As I dont have expertise in programming 
> languages, I found the Galaxy interface very user-friendly for doing such 
> transcriptome analysis. However, I could not find a step wise 
> protocol\workflow for mapping bacterial RNA-seq against the reference genome 
> (we have the completely sequenced genome of our model organism). I have found 
> a detailed step by step workflow for RNA-seq analysis from the University of 
> Alabama web-site (uab.edu). However, it refers to the eukaryotic system.
> Most examples provided and used for analysis are from eukaryotic systems. I 
> am a bit confused weather the same workflow will also work well for bacterial 
> systems as there are no splicing events or I should make some modifications. 
> Can you kindly suggest me which workflow should I follow for mapping the 
> bacterial reads (Bowtie, Tophat or PALMapper) and subsequent quantification 
> steps. I want some guidance in this regard.
> 
> With kind regards,
> 
> Bomba Dam
> -- 
> Dr. BOMBA DAM
> Alexander von Humboldt Postdoctoral Research Fellow
> Max-Planck-Institut für terrestrische Mikrobiologie
> Karl-von-Frisch-Straße 10
> D-35043 Marburg, Germany
> E mail: bomba....@mpi-marburg.mpg.de
> PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 
> (ROOM)
> 
> Assistant Professor of Microbiology
> Department of Botany, Institute of Science
> Visva-Bharati (A Central University)
> Santiniketan, West Bengal 731235, India.
> E mail: bumba_mi...@visva-bhatari.ac.in, bumba_mi...@rediffmail.com;
> 
> 
> 
> 
> 


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