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  1. 10X Genomics
  2. General Single Cell RNA-seq
  3. Software

Software

  • How can I replicate the t-SNE plot in Loupe Cell Browser?
  • How do I prepare Sequence Read Archive (SRA) data from NCBI for Cell Ranger?
  • How does Cell Ranger auto-detect chemistry?
  • How is sequencing saturation calculated?
  • Are the "Mean UMI Counts" from differential expression analysis normalized?
  • Can you repeat cell-calling without re-running cellranger count?
  • How can we add genes to a reference package for Cell Ranger?
  • How does Cell Ranger process and filter UMIs?
  • What version of STAR is used in Cell Ranger?
  • How can I create categories in the .cloupe file from cellranger aggr?
  • Gene Table in Loupe Browser highlight up-regulated genes by default?
  • How can I regress certain genes such as cell cycle genes?
  • How are the UMI counts normalized before PCA and differential expression?
  • What is a barcode whitelist?
  • What are valid barcodes?
  • What parameters are used for STAR index?
  • How does cellranger aggr normalize for sequencing depth among multiple libraries?
  • What does "ERROR; return code from pthread_create() is 11" mean?
  • How does Cell Ranger correct for amplification bias?
  • How were SNVs called in this paper: Massively parallel digital transcriptional profiling of single cells
  • How does Cell Ranger correct barcode sequencing errors?
  • Which reads are considered for UMI counting by Cell Ranger?
  • What contributes to a low transcriptome mapping rate in Cell Ranger?
  • Files and criteria used to generate 10x references?
  • Can I run Cell Ranger on my Mac or Windows machine?
  • How does cellranger count identify multiplets?
  • How are barcodes classified as cell-associated?
  • Can I aggregate gene expression data from different chemistries ?
  • Can low abundance transcripts be detected?
  • How is the MEX format used for the gene-barcode matrices?
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