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 index read, and Read 2.
Specific index information is not required during the sequencing run setup. However, the appropriate number of cycles for the index read needs to be specified (e.g. NNNNNNNN or a generic sequence of 8 nucleotides), which will ensure 8 cycles for the i7 read.
Product-specific sequencing configurations can be found here:
- Genome/Exome: https://support.10xgenomics.com/genome-exome/sequencing
- Single Cell 3': https://support.10xgenomics.com/single-cell/sequencing
- Single Cell V(D)J: https://support.10xgenomics.com/single-cell-vdj/sequencing/doc/specifications-sequencing-requirements-for-single-cell-vdj
- Single Cell ATAC: https://support.10xgenomics.com/single-cell-atac/sequencing/doc/specifications-sequencing-requirements-for-single-cell-atac
A sample sheet is required for demultiplexing. For more information, please see the following pages:
- Genome/Exome: https://support.10xgenomics.com/genome-exome/software/pipelines/latest/using/mkfastq
- Single Cell 3': https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
- Single Cell V(D)J: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/mkfastq
- Single Cell ATAC: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/mkfastq
Note: The MiSeq does not run in standalone mode (e.g. the software generates base call files as the run progresses and writes the data to the output folder location specified for the run).