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Is it possible to use Maq with the latest version of TopHat? I would like to use Maq to align my reads to a reference genome. Then I would like to use TopHat to call RPKM based on the Maq alignments and a supplied GFF3 file. I think the original version of TopHat used Maq as the alignment program, but the current version used Bowtie. Does anyone know what needs to be done to use the Maq output as the alignment in TopHat?
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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