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Have you seen such base distribution plot in BS-seq?
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If by BS-seq you mean Bisulfite Sequencing I have to say NO. Conversion has failed or all Cs were methylated! -
I concur with nucacidhunter and add "Yikes, that's bad!"Comment
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If the experiment is 2x125bp paired-end sequencing and both were concatenated into this one plot and the sequencing is non-directional and you used some kind of target enrichment technique or random primed pull-down then there might be a chance that there is something to be had from the data. But only you would know your library that well...
If this is not the case, I would like to agree with the above posters.
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This plot indicates a very high level of adapter dimer fragments in your library. Filter these out with your favorite trimming/filtering tool and then repeat the base composition plot to see what your valid library fragments look like.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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