Question: Is a sample sheet required for sequencing 10x Genomics' libraries?
Answer: A sample sheet serves two purposes: (1) to instruct the sequencer how many cycles each read should be, and (2) for demultiplexing the sequencing run and generating fastq files corresponding to each sample.
A sample sheet is not required for sequencing 10x Genomics libraries when running the sequencer in 'standalone' mode. However, the run setup must specify the appropriate number of cycles for Read 1, the i7 and i5 index reads, and Read 2. For example, for single index libraries that have an 8bp i7 index sequence, a generic sequence of 8 nucleotides (NNNNNNNN) can be specified for the i7 index read. For dual index libraries that have 10bp i5 and i7 index sequences, a generic sequence of 10 nucleotides (NNNNNNNNNN) can be specified for both the i5 and i7 index reads.
Note for MiSeq: Historically, the MiSeq did not run in standalone mode. However, MiSeq instruments running newer versions of the MiSeq Control Software (MCS) v3.1 and above can be run without a sample sheet. MCS v3.1 added manual mode (similar to standalone mode), which allows users to manually enter run parameters without a sample sheet.
Product-specific sequencing configurations can be found here:
- Spatial Gene Expression
- Single Cell 3'
- Single Cell V(D)J
- Single Cell ATAC
- Single Cell Multiome ATAC+GEX
- Genome/Exome
- Single Cell DNA
A sample sheet is required for demultiplexing after sequencing. For more information, please see the following pages:
- Spatial Gene Expression
- Single Cell 3'
- Single Cell V(D)J
- Single Cell ATAC
- Single Cell Multiome ATAC+GEX
- Genome/Exome
- Single Cell DNA
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell ATAC, Genome/Exome, Single Cell CNV, Chromium Connect, Visium, Visium for FFPE, Single Cell Multiome ATAC+GEX