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Chimeric reads hard clipping
Hello, everyone. I got a question without answer after a long exhaustive liaterature search. I am using multiple displacement amplification (MDA) to amplify my samples, followed by 454 sequencing. MDA is well known for the generation of chimera, and therefore chimeric reads. In my dataset, nearly 30% reads are chimeric, estimated by Bowtie 2 aligner. I wonder whether there are some tools can retrieve the mapped domains of chimeric reads only from SAM output. If yes, I think this may break chimeric reads into single mappable reads.
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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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