Software
- When to run FastQC?
- How can I cite 10x Genomics in my publications?
- Cellranger job failed in stage code exit status 255
- Are the mkfastq pipelines interchangeable between products?
- How can I download older versions of Cell Ranger?
- [error] Barcode out of bounds (I1:0-14)
- 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 run a pipeline on multiple libraries?
- 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?
- How do I demultiplex my data if I only sequenced 7 bp on the index read?
- 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 flowcell?
- How do I run and troubleshoot 10x pipelines on a HPC cluster?
- How do I demultiplex by sample index and barcode?
- [error] No FASTQs matched your sample sheet’s lane, sample, and indexes. Please recheck your sample sheet
- What do I need to demultiplex NovaSeq data?
- 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?