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

Software

  • Why do I not see any fastqs (or see incomplete fastqs) for the SRA of my interest ?
  • Is it possible to do single cell genotyping at a specific locus?
  • How to impute dropouts in scRNAseq data?
  • How to fix ERROR: limitGenomeGenerateRAM is too small for your genome?
  • How is "Log2 fold change" calculated?
  • Which genes are displayed in the Loupe Cell Browser heatmap?
  • How to fix Loupe Browser error "Empty barcode list supplied"?
  • How to resolve mkref error: BUG: next index is smaller than previous, EXITING
  • How can I aggregate or compare single-cell libraries between species?
  • Are there methods for identifying multiplets?
  • Why does cellranger aggr throw an error "Your header row is missing a required field: library_id."?
  • Where are the STAR alignment logs from cellranger count?
  • [Alert] Low Post-Normalization Read Depth
  • How can I identify the 10x library sources when analyzing an aggr matrix using Seurat?
  • Do you have the cell-type annotations for the 1.3M mouse brain cells dataset?
  • How can I identify cells that express Gene A but not Gene B in Loupe Cell Browser?
  • Why did cellranger count fail in the CHUNK_READS stage?
  • How do you select the number of PCs to use for clustering and t-SNE?
  • How do you decompress the 2-bit barcode sequences in molecule_info.h5 file?
  • How can I color the t-SNE plot based on graph-based clustering in cellrangerRkit?
  • Can I generate a 3D t-SNE plot from Cell Ranger output?
  • How to interpret the "Fraction Reads in Cells" metric?
  • How can I modify the STAR alignment parameters in Cell Ranger?
  • Can I generate a matrix h5 file from a molecule_info.h5 file?
  • Why does a warning from cellranger mkref point to an empty list?
  • How can I get read counts for the observed UMIs?
  • How can I color the t-SNE plot by 10x library in cellrangerRkit?
  • What is the AN tag in the BAM file from cellranger count?
  • How can I customize the parameters for k-means and graph-based clustering in Cell Ranger?
  • How can I customize the parameters for t-SNE in Cell Ranger?
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