Hi, my lab is planning to do shotgun metagenomics and metatranscriptomics using Illumina platforms, we want to go for commercial sequencing since we don't have access to HiSeq machine. I'm a beginner in the NGS field and I'm now getting confused on the data size I should get.
The samples come from built environment, what I want to know is the taxonomy and functional gene information from metagenomics and 'active' taxonomy and functioning gene information from metatranscriptomics. I've done a 16S rDNA amplicon sequencing with Illumina MiSeq using some of my DNA samples and they generally contain ~500 different bacteria at the genus level.
The data the sequencing company can give me after sequencing is 'qualified clean data' which seems to be data that index primers are trimmed off and low quality reads are filtered out. The company is suggesting me to get a 3 GB clean data per sample for shotgun metagenomics and a 2-4 GB clean data per sample for metatranscriptomics RNA-seq. I checked for a few metagenomics papers which varies in the data size they acquire (from ~2GB to ~30GB and they do not say if they are raw or clean data).
In this case, could anybody give me some suggestions or experience in approximately how much data (if possible the minimum), or 'clean data' might be enough for the above metagenomics and metatranscriptomics analysis, considering this is a built environment which might not be of high complexity?
Thank you very very much!!!!
The samples come from built environment, what I want to know is the taxonomy and functional gene information from metagenomics and 'active' taxonomy and functioning gene information from metatranscriptomics. I've done a 16S rDNA amplicon sequencing with Illumina MiSeq using some of my DNA samples and they generally contain ~500 different bacteria at the genus level.
The data the sequencing company can give me after sequencing is 'qualified clean data' which seems to be data that index primers are trimmed off and low quality reads are filtered out. The company is suggesting me to get a 3 GB clean data per sample for shotgun metagenomics and a 2-4 GB clean data per sample for metatranscriptomics RNA-seq. I checked for a few metagenomics papers which varies in the data size they acquire (from ~2GB to ~30GB and they do not say if they are raw or clean data).
In this case, could anybody give me some suggestions or experience in approximately how much data (if possible the minimum), or 'clean data' might be enough for the above metagenomics and metatranscriptomics analysis, considering this is a built environment which might not be of high complexity?
Thank you very very much!!!!
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