![]() Illumina® HiSeq 2500 Rapid Run and High Output.If sequencing Single Cell 3’ v3/v3.1 CRISPR Screening Libraries independently, they may be sequenced in a 28 x 8 x 70 bp configuration. **If sequencing 3' v3/v3.1 Cell Surface Protein libraries independently, they may also be sequenced in a 28 x 8 x 25 bp configuration. We recommend pooling Single Cell 3' v3/v3.1 Feature Barcode libraries with Single Cell 3' v3/v3.1 Gene Expression libraries to maintain nucleotide diversity during sequencing. We do not recommend sequencing 10x Single Cell 3’ v3/v3.1 Feature Barcode libraries with a dual-index configuration. Single Cell 3' v3/v3.1 Gene Expression with Feature Barcode technologyĭual Indexed Sequencing Run: Single Cell 3' v3/v3.1 Feature Barcode libraries are single-indexed. Additional bases in Cell barcode or UMI reads will automatically be ignored by Cell Ranger 1.3 or later. Additional bases in Sample index reads must be trimmed using cellranger mkfastq or Illumina's bcl2fastq prior to further analysis. Cell barcode, UMI and Sample index reads must not be shorter than indicated. **Shorter transcript reads may lead to reduced transcriptome alignment rates. We do not recommend sequencing 10x Single Cell 3’ v3/v3.1 libraries with a dual-index configuration. Recommended Sequencing: Minimum 20,000 read pairs/cell*ĭual Indexed Sequencing Run: Single Cell 3' v3/v3.1 libraries are single-indexed. The Chromium™ Single Cell Gene Expression Solution with Feature Barcode technology produces Illumina® sequencer-ready libraries. We do not recommend sequencing Single Cell 3’ v3.1 Dual Index CRISPR Screening or Cell Multiplexing Libraries independently. **If sequencing 3' v3.1 Dual Index Cell Surface Protein libraries independently, they may also be sequenced in a 28 x 10 x 10 x 25 bp configuration. We recommend pooling Single Cell 3' v3.1 Dual Index Feature Barcode libraries with Single Cell 3' v3.1 Dual Index Gene Expression libraries to maintain nucleotide diversity during sequencing. We do not recommend sequencing 10x Single Cell 3’ v3.1 Dual Index Feature Barcode libraries with a single-index configuration. Recommended Sequencing: Minimum 5,000 read pairs/cell*ĭual Indexed Sequencing Run: Single Cell 3' v3.1 Dual Index Feature Barcode libraries are dual-indexed. Single Cell 3' v3.1 Dual Index Gene Expression with Feature Barcode technology ![]() The Sequencing Saturation metric and curve in the Cell Ranger run summary can be used to optimize sequencing depth for specific sample types (note: this metric was named cDNA PCR Duplication in Cell Ranger 1.1 or earlier). *Adjust sequencing depth for the required performance or application.
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