I've just had a very weird MiSeq run pop up, and there are really several things that could be wrong with it - low diversity library, V2 kit (expired), and likely drastically underloaded. The pass filter rate was just terrible. I've never seen the Q score trace look like this, though. Does anyone have any ideas? I'm just interested in getting a diagnosis at this point....
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Given there's a bunch of bases that start with low Q-scores and continue with low Q-scores, I wonder if there's a particular tile on the flow cell that was dirty or otherwise gave bad data. On Basespace/SAV I'd go to the Flowcell Chart and select "Median Q-Score" and look at a handful of cycles to see if certain tiles are consistently giving lousy Q-scores. Also, don't forget to select 'Both Surfaces' (unless you used a nano flow cell in which case you only image one surface).
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...Today, 06:46 AM -
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