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Old 05-22-2017, 01:07 PM   #1
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Location: Buenos Aires, Argentina

Join Date: May 2017
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Default Studying soil microbial communities

I will sequence DNA and RNA from grassland soils using Illumina HiSeq to see differences in composition and functionality (removing 16S). I will use DNA sequencing as a reference to align RNA. I need to establish the paramenters to do the senquencing, 2x100? 2x140? 2x200? I also need to know the minimum reads per sample I will need to see reliable results... 20M? 45M? 60M?
xlopez is offline   Reply With Quote
Old 05-23-2017, 09:34 AM   #2
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Location: CT

Join Date: Apr 2015
Posts: 242

JGI has been sequencing lots of soils. Why don't you download some of their data and subsample the data to evaluate read # needed
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
thermophile is offline   Reply With Quote

metagenome, soil, transcriptome

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