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Does anybody know how to deal with data like this. What's worse, all of the data was generated around repeat elements. Alignment was good, but rmdup could reduce >50% data, and snp calling has a very high false positive rate.
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New library prep? -
Thank you, but I donot quite understand. This is the data they asked me to analyze, so I cannot improve the result by modifing experiment conditions.Originally posted by genericforms View PostComment
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you should first tell us what kind of data you have??
NGS data for ChiP-seq, RNA-seq?
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see this http://seqanswers.com/forums/showthr...cates+chip-seqComment
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50% duplicates is not at all uncommon, it is impossible to tell whether it is worrying or not without details about how the data were generated.Comment
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Something like target specific sequence PCR sequencing, but the target is not unique.Originally posted by harryzs View PostComment
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Yes, the phenomena is not uncommon. But in my case duplicates could leads to very serious misalignment problems and genotype calling errs.Originally posted by kopi-o View PostComment
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Then I would suggest to remove the duplicates with Picard MarkDuplicates.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...Yesterday, 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 -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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