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Which one is preferable in NGS? Using different software for secondary and tertiary analyses or using one complete software package for both of the above? Waiting for some lights to be thrown of.............
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There is no such thing that one tool/ software for all your needs. I have seen people doing mistakes. It will depend on what your questions are e.g in Chip seq histone modification and transcription factor are two different kinds of analysis though basic concept is similar (in layman- no of reads in a particular region) -
Hey Honey.. Thnx for your getting back on this.. I put the question from a different point of view..You have two options to go for:
1. You have a suite/ soft package which performs all basic analyses before going downstream, say, de novo assembly or reference guided alignment etc and also doing all those downstream analyses you are concern about (as you said, ChIP, gene expression analysis) in a interoperable manner.
2. You have to use a software for performing assembly, alignment etc and a different software for your concerned downstream experiment.
So, which one you would go for? A soft package or different soft?
So far I think, there may be some compatibility issues between output of a software and input of next required software, which have to be solved by some conversion tool.
Don't you think here researchers may face some troble in converting the formats?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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