Basepair Support

Getting Started 9

• A Brief Overview of Basepair Features
• How to Upload a Sample to Basepair
• How to Run a New Analysis on Basepair
• Finding and Navigating Your Analysis Results
• How To Share Data With Collaborators On Basepair

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Accounts and Billing 6

• Setting up billing
• Adding users to your billing account
• Credit Card and Usage
• Adding a New User to Your Billing Account
• Creating a new Coupon code to give your customers access to the portal

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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

Running Analyses 1

• Copying data to GEO

Results 11

• RNA-Seq Alignment and QC
• RNA-Seq Differential Expression analysis
• ChIP-Seq Alignment and QC
• ChIP-Seq macs2 peak analysis
• ATAC-Seq alignment and QC

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API 4

• Setup
• Command Line API
• Python API
• Automating NGS projects

Creating a Workflow 3

• Creating a custom workflow on Basepair
• Dockerizing your pipeline
• Storing your docker images

Error Codes 8

• Error ID 1 - Wrong File Type
• Error ID 2 - No peaks found
• Error ID 4 - No mapped reads
• Error ID NA - unknown
• Error ID 11 - Failed to estimate expression variance

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