Software
- 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?
- Why do I see an error about needing consistent R1 length in Cell Ranger 5.0.0
- Does Cell Ranger distinguish between v3 and v3.1 chemistry?
- How to format v1 chemistry datasets to work with current cellranger 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?
- Why is there a discrepancy in the 3M-february-2018.txt barcode whitelist?
- Can I use Cell Ranger to analyze cell hashing data?
- How can I exclude poor quality cells such as cells 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 expression profile of 3' Single Cell v3 chemistry as compared to v2 chemistry
- What is the upper limit of the number of cells that "cellranger aggr” can work with?
- What format of 10x Genomics data should I submit to NCBI GEO?
- How can I convert the feature-barcode matrix from Cell Ranger 3+ to a CSV file?
- Can we detect splice variants or isoforms using single cell 3’ RNA-seq data?
- How can I convert the gene-barcode matrix from Cell Ranger 1.x and 2.x to a CSV file?
- How do I get the read counts for each barcode?
- How to view aggregated .cloupe file by library?
- Does Cell Ranger need the I1 FASTQ file to run?
- How can the percentage of reads aligned to "Exonic Regions" be greater than those aligned to the "Transcriptome"?
- Can I use the 2D t-SNE space to interpret gene expression between clusters?
- What criteria should I use with the mkgtf tool when making a custom reference for Cell Ranger?
- What to do if I sequenced more bases than required on the R1, R2, or the index read for 3' single-cell data?