Studying soil microbial communities

xlopez · 05-22-2017, 01:07 PM

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?

thermophile · 05-23-2017, 09:34 AM

JGI has been sequencing lots of soils. Why don't you download some of their data and subsample the data to evaluate read # needed

05-22-2017, 01:07 PM	#1
xlopez Junior Member Location: Buenos Aires, Argentina Join Date: May 2017 Posts: 1	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?

05-23-2017, 09:34 AM	#2
thermophile Senior Member Location: CT Join Date: Apr 2015 Posts: 233	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.