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how to identify the ideal -c "minimum number of alignments in a locus for needed to conduct significance testing" (--min-alignment-count) to be used in cuffdiff?
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I want to find out too, the default is 1000. How do we set the best value for different RNA-Seq data? Anyone can answer this? -
The default, when using Galaxy, is set to 1000. However, the documentation says this value is set to 10 by default. I'm curious as to this discrepancy and the best value for RNA Seq experiments.
-c/--min-alignment-count <int> The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 10 fragment alignments.Comment
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Hi, yes, I noticed that too... was it a mistake on the documentation or on Galaxy? but I had set 100 on my data.Comment
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Galaxy just changed it to 10, seems a mistake.Comment
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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.
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