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Frequently Asked Questions (FAQ)
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?
What does it mean when a set of genes are positively correlated versus negatively correlated in the GSEA analysis? Does positively correlated mean those genes are upregulated in the sample?
I already completed some analysis of my data and have an expression matrix of read counts. Can I upload that data into Basepair for further analysis?
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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 is the purpose of motif analysis?
I want to draw the control and treated samples in the same heatmap. How can I do that?
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Single Cell RNA-Seq FAQ
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?
Do you check the relationship between nUMI vs nGenes plot? Do you have a specific threshold in this graph?
What quality control metrics are important in ATAC-seq data?
What is the difference between coverage and read depth? How many reads do you need for ATAC-seq data?
What is the expected duplication rate for ATAC-seq data?
Do you need paired end data for ATAC seq?
I only have single end reads for my ATAC-seq analysis. Can I salvage the data?
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Celllranger Single Cell RNA-Seq FAQ
How To Create Feature Reference CSV File For Cellranger Feature Barcode Analysis