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Naive question. I do not quite understand in what situations the postprocessing option -g would be useful (use gapped alignments when attempting to rescue pairs). Thoughts?
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If you are trying to rescue the other read considering the to-be-rescued end with indels the gapped method is useful. I find that it overfits by calling falsely indels in many cases. Remember, the rescue relies solely on its pair/mate.Originally posted by Protaeus View Post
I would test both out and see which you are most happy with. Always good to have options (literally).
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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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