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BASEPAIR SUPPORT Welcome Login Sign up Home Solutions HOW CAN WE HELP YOU TODAY? Enter your search term here... Search Login or Signup to submit a new ticket Check ticket status 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 Home Solutions