Specifications, Last Modified on June 29, 2018, Permalink
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|
** 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