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BASEPAIR SUPPORT

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HOW CAN WE HELP YOU TODAY?

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KNOWLEDGE BASE


GENERAL TUTORIALS

Getting Started 8
 * 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

See all 8 articles
Accounts and Billing 4
 * Setting up billing
 * Adding users to your billing account
 * Credit Card and Usage
 * Adding a New User to Your Billing Account


FREQUENTLY ASKED QUESTIONS (FAQ)

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?

See all 10 articles
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?

See all 7 articles
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?

See all 11 articles
Celllranger Single Cell RNA-Seq FAQ 1
 * How To Create Feature Reference CSV File For Cellranger Feature Barcode
   Analysis


ANALYSES

Running Analyses 1
 * Copying data to GEO

Results 5
 * ChIP-Seq Results
 * DNA-Seq Results
 * RNA-Seq Results
 * DEseq Interactive Plotting
 * Trimming, Alignment, Expression Quantification & Differential Expression


ADVANCED TUTORIALS

API 3
 * Python API
 * Command line API
 * Automating NGS projects

Creating a Workflow 4
 * Overview
 * Define Modules
 * Define Workflow
 * Test


ERRORS

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

See all 8 articles
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