Software
- 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 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 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 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?
- Why do I see more MT-enriched cells from Cell Ranger 3+ compared to Cell Ranger 2?
- Do we see a difference in the expression profile of 3' Single Cell v3 chemistry compared to v2 chemistry?
- What is the upper limit for the number of cells that cellranger aggr can work with?
- What format of 10x Genomics data should I submit to NCBI GEO/SRA?
- How can I convert the feature-barcode matrix from Cell Ranger 3+ to a CSV file?