Basepair Support

RNA-Seq FAQ 10

• 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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ChIP-Seq FAQ 7

• 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 4

• 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?

ATAC-Seq FAQ 11

• 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 1

• How To Create Feature Reference CSV File For Cellranger Feature Barcode Analysis