General Tutorials (2)
Video tutorials to help you quickly start using Basepair
Frequently Asked Questions (FAQ) (4)
Running an analysis and have a question? Check out the FAQs. We may already have an answer.
-
Where can I find and change the default trimming settings for an RNA-seq analysis?
-
I see what looks like an outlier sample in my PCA plot. What should I do? Should I exclude the sample from the analysis?
-
What is the difference between the Wald test and the Likelihood Ratio Test (LRT), and which is preferred?
-
If I have a unique alignment rate of 20%, does that mean my samples are contaminated?
-
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?
-
If my samples don't have a spike-in, is the CHIP-seq data still going to be reliable?
-
What tools do you use in Basepair's single cell pipeline?
-
Can I upload two samples of single cell RNA-seq data (treatment and control) and compare them?
-
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?