Software
- 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?
- Are the mkfastq pipelines interchangeable between products?
- How can I download older versions of Cell Ranger, Loupe Browser, or other 10x software?
- [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
- How to filter the BAM file produced by 10x pipelines with a list of barcodes?
- How to convert 10x BAM files to FASTQ files while preserving the barcode information?
- How do I identify the unmapped reads in my Cell Ranger or Long Ranger output?
- What bcl2fastq parameters does mkfastq use internally?
- What is Martian?
- How do I get help with a failed mkfastq run?
- Should I use the IEM or simple CSV format sample sheet for demultiplexing with mkfastq?
- How to input FASTQ files from resequenced libraries?