Software
- GEM-X Universal Multiplex (or OCM) Barcode lists and understanding its usage
- What are the differences in barcode inclusion list (formerly barcode whitelist) names for 3' assays in Cell Ranger v9.0?
- What are the differences in the GRCm38 and GRCm39 mouse references? Which one should I use?
- Species Cell Assignments on Loupe for Barnyard samples
- My samples are analyzed with Cell Ranger v7.2. Should I upgrade to using the latest Cell Ranger v8.0?
- Unable to detect certain markers like GFP, mCherry or tdTomato in my single cell data
- Should I upgrade Cell Ranger to v7.1 for cell multiplexing analysis?
- What are the cell calling updates in Cell Ranger v7.1 and its impact on Single Cell Gene Expression data?
- Is filtering of ribosomal and mitochondrial genes in nuclei data needed?
- Nuclei aggregates in a barcode rank plot
- Why are some mapping metrics in Cell Ranger higher for nuclei data?
- Can we aggregate nuclei and cellular data on Cell Ranger aggr?
- Common mkref formatting errors when building custom reference from NCBI, UCSC or RefSeq genomes
- How to troubleshoot Cell Ranger count Segmentation Fault (Duplicate contigs)?
- What if wrong chemistry was detected for my 3’ LT (Low Throughput) v3.1 library?
- Loupe file not found when you execute aggr (count, multi) due to a CSV formatting issue
- How to extract multi-mapped reads from Cell Ranger BAM files ?
- How do you split a large Loupe file into smaller files?
- Does my genome sequence needs be masked or unmasked for custom reference generation ?
- Can I use aggr to combine 3’ LT v3.1 data with standard 3’ v3.1 data? Will there be chemistry batch effects?
- Does 3’ LT (Low Throughput) v3.1 chemistry use a separate barcode inclusion list (barcode whitelist)?
- How to resolve this error "We detected a mixture of different R1 lengths"?
- Does Cell Ranger distinguish between v3 and v3.1 chemistry?
- How to format v1 chemistry datasets to work with current Cell Ranger versions?
- How can I add SARS-CoV-2 to the pre-built human GRCh38 reference?
- What is the Median Normalized Average statistic in Loupe Browser in the differential gene expression table?
- Why is there a discrepancy in the 3M-february-2018.txt barcode inclusion list (formerly barcode whitelist)?
- What parameters are used for STAR alignment?
- Can I use Cell Ranger to analyze cell hashing data?
- How can I exclude poor quality cells such as those that show enrichment of MT genes?