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Question: RNAseq analysis for Bacterial genomes
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gravatar for palmer.750
2.8 years ago by
palmer.750 • 0
palmer.750 • 0 wrote:

Hello,

I am interested in using the tuxedo suit to analyze RNAseq data from the bacteria Streptococcus mutans (2MB genome no introns). However, many of the parameters are designed to be used with eukaryotic data, which has exons and introns. Is there a recommended parameter list for this sort of analysis. I haven't been able to find a pipeline online. 

Thanks,

palmer.750

 
bacterial rnaseq • 793 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by palmer.750 • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The Tuxedo tool suite is tuned for mammalian genomes and is probably not the best choice. There are many publications that tackle the subject (google or other pub search).

I suggest reviewing the latest publications, comparing against the tools available in the Tool Shed, then creating your own pipeline. If there is a particular tool that you want to use that isn't already wrapped for Galaxy, it could be, if you are able to do that or have informatics resource to help.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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