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Dear All
I haven't previously had any reason to apply NGS in my research but do now and am finding I've been left behind a bit! So - and I am reading all I can including posts here - please be kind! I am writing a grant application that was designed, initially, to use just 16S rRNA phylogenetic profiling to compare species abundances in gut microbiota between patients in a group with a specific metabolic disorder and matched controls. It was subsequently suggested that some form of metabolic network analyses might be usefully applied and that this would preferably require shotgun metagenomic data be obtained in addition to the 16S.
Would applying both these approaches be justified in that they would/should provide different but complementary data sets?
I am interested in a specific metabolic pathway mediated by the gut microbiota and would like to determine whether this pathway is over/under represented in the microbiota between the two groups. Should we concentrate on reassembling just this KEGG-annotated pathway from the shotgun metagenomic data or is there a more global metabolic network analysis scheme that could be applied that would not only reveal any differences in this specific pathway but would, in addition, provide insight into any other differences in the metabolic capacity of the gut microbiota between test and control groups?
Lastly, there appear to be a plethora of different software methods to clean, filter, QC the original sequence data before its considered fit to use. Is there any sort of a 'flow-chart' that would guide a beginner through these options?
I haven't previously had any reason to apply NGS in my research but do now and am finding I've been left behind a bit! So - and I am reading all I can including posts here - please be kind! I am writing a grant application that was designed, initially, to use just 16S rRNA phylogenetic profiling to compare species abundances in gut microbiota between patients in a group with a specific metabolic disorder and matched controls. It was subsequently suggested that some form of metabolic network analyses might be usefully applied and that this would preferably require shotgun metagenomic data be obtained in addition to the 16S.
Would applying both these approaches be justified in that they would/should provide different but complementary data sets?
I am interested in a specific metabolic pathway mediated by the gut microbiota and would like to determine whether this pathway is over/under represented in the microbiota between the two groups. Should we concentrate on reassembling just this KEGG-annotated pathway from the shotgun metagenomic data or is there a more global metabolic network analysis scheme that could be applied that would not only reveal any differences in this specific pathway but would, in addition, provide insight into any other differences in the metabolic capacity of the gut microbiota between test and control groups?
Lastly, there appear to be a plethora of different software methods to clean, filter, QC the original sequence data before its considered fit to use. Is there any sort of a 'flow-chart' that would guide a beginner through these options?
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