Question: How does cellranger count auto-detect the assay chemistry?
Answer: To auto-detect the assay chemistry (--chemistry=auto), cellranger count maps the first 10,000 reads in the FASTQ files.
The 3' versus 5' assay configurations are inferred based on the dominant orientation of the R2 read mapping (from at least 1,000 mapped reads). For example, if antisense is greater than sense mapping for the R2 read, the library is inferred to be a 5' gene expression assay.
The distinction between Single Cell 3' v1 and v2 chemistries is made based on the fraction of barcodes overlapping the whitelist for each specific chemistry.
The chemistry settings can be nested as shown below: threeprime or fiveprime auto-detect options within the 2 possible assay configurations (3' or 5'), respectively. Within 3' or 5', there are versions of the assay and alignment options which can also be directly specified.
auto:
- threeprime for Single Cell 3':
- SC3Pv1 for Single Cell 3' v1
- SC3Pv2 for Single Cell 3' v2
- fiveprime for Single Cell 5':
- SC5P-PE for Single Cell 5' paired-end (where both R1 and R2 are used for alignment)
- This can be used if you sequenced R1 longer than 28 bases
- SC5P-R2 for Single Cell 5' R2-only (where only R2 is used for alignment)
- This assumes the recommended sequencing configuration
- SC5P-R1 for Single Cell 5' R1-only (where only R1 is sequenced).
- SC5P-PE for Single Cell 5' paired-end (where both R1 and R2 are used for alignment)
For more information pease consult the Cell Ranger documentation.