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Old 06-02-2016, 06:56 AM   #1
chc*
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Location: Devon, UK

Join Date: Jan 2016
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Default Read counting and DESeq versus read abundance with MG-RAST

Hi all.
I am planning a metatranscriptomics experiment to investigate the changes in community and metabolic function of a Chlorella culture and it's associated bacterial consortium. Practical aspects of preparing the libraries aside, I want to gain some clarity on the following:
Do I go for simple mapping of reads to annotated genes using MG-RAST then use the abundance automatically computed here for statistical inference of changes in transcript abundance? Alternatively, i can sequence the metagenome. My understanding is that if it is simple I can then map the RNAseq metatranscriptomic reads to a metagenomic assembly (or assembled genomes found within the metagenome) then use HTseq count and DESeq for DE analysis.
What are the pros and cons/ what are the reasons for chosing one or the other please?
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