Software
- In Loupe Browser, why is the average in Feature Table different from the mean in Violin Plots?
- I used antibody tags for cell surface protein capture and cell hashing with Single Cell 3' chemistry. How can I use Cell Ranger to analyze my data?
- I have multiplexed multiple samples in 5'GEX with TCR/BCR libraries. Can I use Cell Ranger to demultiplex the samples ?
- Can I remove ambient RNA contamination from cells in my gene expression data ?
- How do I find out which FASTQ files belong to which library in 10x Genomics bamtofastq output folders?
- Which CellPlex data files should be uploaded/downloaded to/from public repositories such as GEO/SRA?
- How can I annotate the cell types from scRNA-seq data?
- How can I use the filter function in Loupe Browser?
- How do I create cell clusters using the Feature Plot in Loupe Browser?
- How do I use the split view function in Loupe Browser?
- Can I use mkfastq to demultiplex single indexed libraries
- How can I demultiplex a flowcell with both single and dual indexed libraries pooled in one lane?
- Why do I not see any FASTQs (or incomplete FASTQs) for the SRA of my interest ?
- [error] No input FASTQs were found with the requested sample indices.
- 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 Cell Ranger?
- [Alert] Low Post-Normalization Read Depth
- How can I identify the 10x library sources when analyzing an aggr matrix?
- 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?