Question: I have sequenced my 10x Genomics libraries on the Element AVITITM System. Will my FASTQ files be compatible for software analysis?
Answer: If the Element AVITI System is used for sequencing, Element’s bases2fastq demultiplexing software must be used to generate FASTQ files. The mkfastq pipeline cannot be used because it is a wrapper around Illumina’s bcl2fastq. As long as the 10x product-specific sequencing read lengths and FASTQ filename requirements are met, then FASTQ files generated from AVITI data should be compatible as inputs to downstream 10x Genomics analysis software pipelines without further processing needed.
For troubleshooting the demultiplexing and FASTQ generation process, 10x Genomics is not able to provide support. Please contact Element support: support@elembio.com. If there are questions or errors related to 10x analysis software pipelines, please contact 10x support support@10xgenomics.com.
Each 10x Genomics assay has its own requirements for sequencing lengths. Please see product-specific pages for further information:
- Chromium Single Cell Gene Expression
- Chromium Immune Profiling
- Chromium Single Cell Gene Expression Flex
- Chromium Single Cell Mulitome ATAC + Gene Expression
- Chromium Single Cell ATAC
- Visium Spatial Gene Expression for FFPE
- Visium Spatial Gene Expression for Fresh Frozen
- CytAssist Spatial Gene Expression
- CytAssist Spatial Gene Expression and Protein Expression
- HD Spatial Gene Expression
When sequencing with AVITI, this file naming format can be achieved by adding the argument --legacy-fastq to the bases2fastq command. This will apply a legacy file naming convention to the output FASTQ files, such as SampleName_S1_L001_R1_001.fastq.gz. For further information on running the bases2fastq software, please go to this link https://docs.elembio.io/docs/bases2fastq/ or contact Element support: support@elembio.com.
For each 10x analysis software pipeline, the FASTQ filenames must follow this general format:
Each 10x Genomics product has its own software analysis pipeline. The specifying FASTQs pages linked below explain what FASTQ files are required as input for each 10x analysis software pipeline.
Cell Ranger >v7.0.0
Chromium Single Cell Gene Expression
Chromium Single Cell Immune Profiling
Chromium Single Cell Gene Expression Flex
Space Ranger >v2.0.0
Visium Spatial Gene Expression for FFPE
Visium Spatial Gene Expression for Fresh Frozen
Visium CytAssist Spatial Gene Expression and Protein Expression
HD Spatial Gene Expression
Cell Ranger ARC
A revised version of this analysis software pipeline is required to accommodate Phred quality scores >40, such as those from the Element AVITI System. At this time, the latest version of Cell Ranger ARC v2.0.2 is unable to accommodate AVITI FASTQ files, and you will get an error "Invalid quality value". Please contact support@10xgenomics.com to obtain this revised version.
Chromium Single Cell Multiome ATAC + Gene Expression
Cell Ranger ATAC
A revised version of this analysis software pipeline is required to accommodate Phred quality scores >40, such as those from the Element AVITI System. At this time, the latest version of Cell Ranger ATAC v2.1.0 is unable to accommodate AVITI FASTQ files, and you will get an error "Invalid quality value". Please contact support@10xgenomics.com to obtain this revised version.
Chromium Single Cell ATAC
Please note that neither Chromium Single Cell ATAC nor Chromium Single Cell Multiome ATAC + Gene Expression have been tested nor validated by 10x Genomics for sequencing on the Element AVITI System.
For further information about what 10x Genomics library types have been verified as compatible with sequencing on the Element AVITI System, see this article: