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  1. 10X Genomics
  2. Single Cell Gene Expression
  3. Software

Software

  • Should I upgrade Cell Ranger to v7.1 for cell multiplexing analysis?
  • What are the cell calling updates in Cell Ranger v7.1 and its impact on Single Cell Gene Expression data?
  • Is filtering of ribosomal and mitochondrial genes in nuclei data needed?
  • Nuclei aggregates in a barcode rank plot
  • Why are some mapping metrics in Cell Ranger higher for nuclei data?
  • Can we aggregate nuclei and cellular data on Cell Ranger aggr?
  • Common mkref errors when building custom reference from NCBI, UCSC or RefSeq genomes
  • How to troubleshoot Cell Ranger count Segmentation Fault (Duplicate contigs)?
  • What if wrong chemistry was detected for my 3’ LT (Low Throughput) v3.1 library?
  • Loupe file not found when you execute aggr (count, multi) due to a CSV formatting issue
  • How do you split a large Loupe file into smaller files?
  • Can I aggregate CellPlex samples with non-CellPlex samples?
  • Does my genome sequence needs be masked or unmasked for custom reference generation ?
  • Can I use aggr to combine 3’ LT v3.1 data with standard 3’ v3.1 data? Will there be chemistry batch effects?
  • Does 3’ LT (Low Throughput) v3.1 chemistry use a separate barcode whitelist?
  • How to resolve this error "We detected a mixture of different R1 lengths"?
  • Does Cell Ranger distinguish between v3 and v3.1 chemistry?
  • How to format v1 chemistry datasets to work with current Cell Ranger versions?
  • How can I add SARS-CoV-2 to the pre-built human GRCh38 reference?
  • What is the Median Normalized Average statistic in Loupe Browser?
  • Why is there a discrepancy in the 3M-february-2018.txt barcode whitelist?
  • What parameters are used for STAR alignment?
  • Can I use Cell Ranger to analyze cell hashing data?
  • How can I exclude poor quality cells such as those that show enrichment of MT genes?
  • Why do I see more MT-enriched cells from Cell Ranger 3+ compared to Cell Ranger 2?
  • Do we see a difference in the expression profile of 3' Single Cell v3 chemistry compared to v2 chemistry?
  • What is the upper limit for the number of cells that cellranger aggr can work with?
  • What format of 10x Genomics data should I submit to NCBI GEO/SRA?
  • How can I convert the feature-barcode matrix from Cell Ranger 3+ to a CSV file?
  • Can we detect splice variants or isoforms using single cell 3’ RNA-seq data?
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