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Old 04-15-2013, 09:49 AM   #2
Genome Informatics Facility
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default metatranscriptome

Originally Posted by Tka View Post

I am new to RNA-seq analysis and wanted to ask for some advice. I'm working on several soil metagenomes taken at different temperatures. My plan is to map the reads from each sample against a reference genome and subsequently use DeSeq and Edger to screen for differentially expressed genes.
I was wondering if this will give reasonable results as I am only working with those metagenome reads that map to the reference. What do you think?

To get a proper answer you will need to provide a lot more information about how deep the sequences was, if this is an environmental sample or sterilized a with reference bacteria added, and how many biological replicates do you have?

Let's assume these are environmental samples, then I would recommend doing de novo assembly and mapping back to the assembly to get count data.

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