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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
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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Copying data to GEO
RNA-Seq Alignment and QC
RNA-Seq Differential Expression analysis
Single cell RNA-seq
Single cell RNA-seq Integrate
ATAC-Seq alignment and QC
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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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Cellranger Single Cell RNA-Seq FAQ (removed 1/1/2024)
Command Line API
Automating NGS projects
Creating a Workflow
Creating a custom workflow on Basepair
Dockerizing your pipeline
Storing your docker images
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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