integration with single cell genomic data #471
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soilmicrobiome
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Good idea to include SAGs. However, I don't have experience with them? What would be a typical workflow for SAGs? |
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I usually treat them like a genome. So i run them with GTDB-Tk, predict genes, annotate and then i read map with the metagenome to get some sense of abundance. But would be cool if they could some how be part of the pipeline just not sure how. |
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Is it possible to run metagenomic samples and SAGs in the same run? Would be nice to have one reconciled genecatalog/abundance table for all the samples (since in my case they are one data set). But for the SAGs they don't need the full pipeline. Is this possible or will the SAGs need to be run separately as "genomes"? Thoughts on how to deal with SAG data, any suggestions?
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