Software
- 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 bamtofastq output folders?
- 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 see 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 cellranger count?
- [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?
- 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?
- Can I generate a 3D t-SNE plot from Cell Ranger output?
- How to interpret the "Fraction Reads in Cells" metric?