ATAC Library Sequencing Depth & Run Parameters
These sequencing parameters are specific for Chromium Single Cell Multiome ATAC libraries and are different from the recommendations for standalone ATAC libraries. Ensure that these specific recommendations are provided to the sequencing service provider.
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Sequencing Depth |
25,000 read pairs per nucleus (25,000 reads for Read 1N; 25,000 reads for Read 2N) |
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Sequencing Type |
Paired-end, dual indexing |
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Sequencing Read |
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Read 1N i7 Index i5 Index Read 2N |
50 cycles 8 cycles 24 cycles* 49 cycles |
*Custom sequencing recipe:
Sequencers that do not support 24 nt read in i5 (e.g. Nextseq™ 500/550) require a custom recipe that includes 8 dark cycles and 16 nt cycles on i5. After installation of custom sequencing recipe, input 16 cycles for i5 read.
It is imperative to use a custom recipe for these sequencers. Entering 16 cycles for i5 read without the use of the custom recipe will cause the sequencing run to proceed but the data will be unusable.
Custom recipe is NOT required for NextSeq™ 1000/2000.
Contact Support@10xgenomics.com for any additional questions.