Software
- 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?
- 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?
- How can I modify the STAR alignment parameters in Cell Ranger?
- Can I generate a matrix h5 file from a molecule_info.h5 file?
- How can I get read counts for the observed UMIs?
- What is the AN tag in the BAM file from Cell Ranger?
- What is the difference between the filtered and raw gene-barcode matrix?
- Why is Martian waiting for jobs to complete when I have plenty of memory available?
- Why am I getting 5' capture of my transcripts on the 3' single- cell assay?
- Why do I see a high level of mitochondrial gene expression?
- Does Cell Ranger automatically exclude doublets?
- Why do I have zero UMI counts for my marker gene?
- How to identify cells that express geneA and geneB in Loupe Cell Browser?
- How can I remove batch effects among samples in Cell Ranger?
- Why do I have a high percentage of reads mapping to intronic regions?
- Can you give more information on the statistical test used for differential expression analysis in Cell Ranger?
- 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?