Software
- 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
- Is there way to filter the BAM file produced by 10x pipelines with a list of barcodes?
- How do I analyze multiple libraries with one command?
- 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?
- How to troubleshoot installing bcl2fastq?
- How to manually generate a .mri.tgz file for a failed run?
- How to demultiplex a single indexed library on a dual indexed flow cell?
- How do I run and troubleshoot 10x pipelines on a HPC cluster?
- How do I demultiplex by sample index and barcode?
- Is mkfastq really needed to demultiplex, or can we use bcl2fastq?
- How do I demultiplex a run with no index sequences?
- What to do if I forgot which sample indices I used during library construction?
- Should I calculate TPM, RPKM or FPKM, instead of counts for 10x Genomics data?