Question: I want to upload my 10x Genomics data to public databases such as NCBI GEO/SRA. What file(s) should I upload?
Answer: The files to submit to public repositories depends on the 10x Genomics workflow/chemistry version used to generate the data. The table below lists the recommended files to submit for different 10x Genomics chemistries. The alternative data type for submission is also listed.
| 10x Genomics Library: Chemistry version | Recommended | Alternative |
|
Gene Expression*: 3' v3.1, 3' LT v3.1, 3' v3, 3' v2, 5' v2, 5' v1.1, 5' v1 |
R1 and R2 FASTQs | 10x BAM |
|
Visium FF & FFPE |
1. R1 and R2 FASTQs; 2. Image (submitted as processed data file) |
1. 10x BAM; 2. Image (submitted as processed data file) |
| Feature Barcode: Cell Surface Protein, CRISPR Screening | R1 and R2 FASTQs | 10x BAM |
| 3' CellPlex** |
10x per-sample BAM (see here) |
N/A |
| 5' TCR/BCR***: v2, v1.1, v1 | R1 and R2 FASTQs | N/A |
| Multiome Gene Expression | R1 and R2 FASTQs | 10x BAM |
| Multiome ATAC**** | 10x BAM | N/A |
| ATAC****: v1.1, v1 | 10x BAM | N/A |
| Chromium Genome, Single Cell DNA | R1 and R2 FASTQs | 10x BAM |
*Note that for 3' v1 chemistry, uploading only R1 and R2 FASTQ files is NOT sufficient for others to reproduce the analysis. In this version, 10x Genomics BAM file is the recommended file.
**For submitting cell multiplexing data, please see Which CellPlex data files should be uploaded/downloaded to/from public repositories such as SRA/GEO?
***10x Genomics V(D)J BAMs do not yet contain all the necessary tags for reversion to original FASTQ data; therefore, uploading R1 and R2 FASTQ files is recommended.
****For 10x Genomics ATAC data, all R1, R2, and R3 FASTQ files are required to perform the single cell analysis, and all relevant information is stored in the BAM file output from the 10x Genomics cellranger-arc or cellranger-atac pipeline. Therefore, uploading the 10x Genomics BAM file is the best way for depositing 10x Genomics ATAC data.
If a 10x Genomics BAM is submitted, future users of the data can convert it back to FASTQ format for new analyses using the 10x Genomics tool bamtofastq.