Software
- My samples are analyzed with Cell Ranger v7.1. Should I rerun analysis using the latest Cell Ranger v7.2?
- My antibody t-SNE shows noodles or worms
- How are data normalized for the multi-sample comparison (pseudo-bulk differential expression) calculation in Loupe Browser?
- What is the minimum number of replicates needed to perform multi-sample (pseudo-bulk) differential gene expression in Loupe Browser?
- What does the error: "all values must be less than 32767" mean when using LoupeR?
- Are my sample’s antisense and intronic reads levels normal or of concern?
- Does mkfastq work with NovaSeq X data?
- FASTQ header mismatch error
- IO error in FASTQ files when running Cell Ranger or Space Ranger pipelines
- Why do I have an alert in my web summary with 'Low Fraction of Valid UMIs'?
- My samples are analyzed with Cell Ranger v7.0. Should I rerun analysis using the latest Cell Ranger v7.1?
- How to generate FASTQs with BCL Convert for 10x gene expression products
- Will mkfastq be affected by the NovaSeq control software upgrade to v1.8.0?
- When is deeper sequencing needed for nuclei data ?
- Is it possible to aggregate nuclei data of higher sequencing depth ?
- ERROR: There were no reads to process.
- What's the "Sum" feature in Loupe Browser?
- Which scale value should I choose in Loupe Browser?
- What adapters should I use in my IEM sample sheet?
- How do I demultiplex a dual index library with only one index
- Are the references interchangeable between pipelines?
- How do I solve for '[error] Formatting error in sample sheet'?
- How to use masking parameter while demultiplexing 10x sequencing data ?
- When to run FastQC?
- I sequenced my dual indexed library as 8bp single index. Can I rescue my data?
- How can I cite 10x Genomics in my publications?
- [error] Barcode out of bounds (I1:0-14) or (I2:0-16)
- How do I fix the mkfastq error "No bcl2fastq found on path"?
- Is it possible to get gene expression values on a cell by cell basis instead of on a cluster by cluster basis in Loupe Cell Browser?
- Create clusters of a given cell type in different samples in a combined cloupe file