Sequencing Requirements for Single Cell DNA

Specifications, Last Modified on June 29, 2018, Permalink

Single Cell DNA Libraries

Supported Sequencers: *

Recommended Sequencing Depth:

Paired-end, single indexing: Single Cell DNA libaries are single-indexed. Although single indexing is recommended, if a dual-index configuration is used, use bcl2fastq’s --use-bases-mask or mkfastq’s --ignore-dual-index option to ignore the I2 read.

Read Read 1 i7 Index i5 Index Read 2
Purpose 16bp 10x Barcode and gDNA Sample Index N/A gDNA
Length ** 100 or 150 8 0 100 or 150

* Sequencing Performance Details

** Sample index reads must not be shorter than indicated. Any read can be longer than recommended. Additional bases in sample index reads must be trimmed using “cellranger-dna mkfastq” or Illumina’s “bcl2fastq“ prior to further analysis. Shorter read lengths will reduce the fraction of genome over which copy number is estimated