10x Genomics
Visium Spatial Gene Expression

Space Ranger1.3, printed on 12/22/2024

Sequencing - Read 2 Length

Visium gene expression & targeted

10x recommends sequencing read 2 to a length of 90 bases.

Space Ranger from v1.1 onwards is less sensitive than previous versions to read length effects. In our experience, the rate at which reads map confidently to a gene, as well as the sensitivity of the resulting analysis, is consistent across a range of read lengths longer than 70 bp. The following graph shows the relationship between read mapping and read 2 length, after trimming, for six representative samples.

Mapped reads is consistent across read lengths over 70 bp after trimming

Visium for FFPE

10x Genomics recommends sequencing read 2 to a length of 50 bases.

For formalin fixed paraffin embedded (FFPE) tissue the construct is of a known length. Since the reads are aligned to the reference, read 2 length shorter than 50 bases can lead to decreased performance.

Common FAQs

• Sequencing parameters for fresh frozen libraries
• Suggested sequencing depth for fresh frozen libraries
• Sequencing parameters for FFPE libraries
• Suggested sequencing depth for FFPE libraries