Software
- What are valid barcodes?
- What parameters are used for STAR index?
- How does cellranger aggr normalize for sequencing depth among multiple libraries?
- What does "ERROR; return code from pthread_create() is 11" mean?
- How does Cell Ranger correct for amplification bias?
- How were SNVs called in this paper: Massively parallel digital transcriptional profiling of single cells
- Which reads are considered for UMI counting by Cell Ranger?
- What contributes to a low transcriptome mapping rate in Cell Ranger?
- Files and criteria used to generate 10x references?
- Can I run Cell Ranger on my Mac or Windows machine?
- How does cellranger count identify multiplets?
- How are barcodes classified as cell-associated?
- Can I aggregate gene expression data from different chemistries ?
- Can low abundance transcripts be detected?
- How is the MEX format used for the gene-barcode matrices?
- How do I analyze exogenous RNA transcripts?
- What fraction of reads map to ribosomal proteins?
- What is t-Distributed Stochastic Neighbor Embedding (t-SNE)?
- Are UMI counts comparable between samples?