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Old 06-03-2019, 09:21 PM   #1
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Location: japan

Join Date: Apr 2018
Posts: 2
Default summary statistics of metagenomics

Hey All

I want to represent my 200 metagenome assemblies and preliminary analysis in a table. I was wondering if the following data are a good representation of summary statistics for metagenomes?

a) Average of (Number of contigs assembled per metagenome) #from SPAdes
b) Average of (N50 of contigs per metagenome) #from QUAST
c) Average of (% of bacterial reads per metagenome) #from MG-RAST analysis
d) Average of (% of reads for top bacterial functions) #from MG-RAST
e) Average of (% of genes annotated as bacteria) #from PROKKA?
I want to do this, but how do I find if a gene predicted as bacteria is a spurious hit or not? Is there any significance test?

What other measures can I use to show if my metagenomes are sequenced and assembled "correctly"?
jigyasa is offline   Reply With Quote

metagenome assembly, mg-rast, prokka

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