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Where can I find and change the default trimming settings for an RNA-seq analysis?
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I see what looks like an outlier sample in my PCA plot. What should I do? Should I exclude the sample from the analysis?
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What is the difference between the Wald test and the Likelihood Ratio Test (LRT), and which is preferred?
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If I have a unique alignment rate of 20%, does that mean my samples are contaminated?
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When spike-in control chromatin cannot be included, what is the best way to normalize two or more samples that have different enrichments and/or different number of reads?
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If my samples don't have a spike-in, is the CHIP-seq data still going to be reliable?
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What tools do you use in Basepair's single cell pipeline?
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Can I upload two samples of single cell RNA-seq data (treatment and control) and compare them?
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How do you account for technical variability? Does the program fit for mean variance trend, test for non zero biological variability, or deconvolution based normalization?