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  1. 10X Genomics
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Software

  • 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
  • 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?
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