Software
- What do the percentages mean in the barcode rank plot?
- Is it required to sequence more for nuclei compared to cells ?
- Should I include introns for Targeted Gene Expression data analysis?
- Can I aggr data run with and without introns?
- Can I sequence less if I use intronic mode?
- I do not want to include intronic reads in my analysis. Can I do that in Cell Ranger?
- Does data analyzed with intronic reads have biases as compared to data analyzed without intronic read counting?
- Should I reanalyze my previous single cell data, if I have not included introns before?
- Why should I include introns for my single cell whole transcriptome Gene Expression data analysis?
- 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