Software
- How to convert 10x BAM files to FASTQ files while preserving the barcode information?
- Should I trim the reads in my FASTQ files?
- 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?
- What is the difference between mkfastq, bcl2fastq, and demux?
- How to troubleshoot installing bcl2fastq?
- What is an MRO file?
- Can I combine BCL files from different sequencers (NovaSeq and NextSeq)?
- Is mkfastq interchangeable between 10x pipelines?
- Can 10x Genomics pipelines run on non Linux operating systems?
- How to manually generate a .mri.tgz file for a failed run?
- How to demultiplex 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?
- 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?