Question: I want to upload my 10x Genomics data to public databases such as NCBI GEO, SRA. What file(s) should I upload?
Answer: What files to be submitted to public repositories will depend on what 10x workflow/chemistry version was used to generate the data. The table below lists the recommended files to submit for different 10x chemistries. The alternative data type for submission is also listed.
|10x 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|
|Feature Barcode: Cell Surface Protein, CRISPR Screening||R1 and R2 FASTQs||10x BAM|
10x per-sample BAM
|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 BAM file is the recommended file.
**For how to submit cell multiplexing data, please see Which CellPlex data files should be uploaded/downloaded to/from public repositories such as SRA/GEO?
***10x VDJ 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 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 cellranger-arc or cellranger-atac pipeline. Therefore, uploading the 10x BAM file is the best way for depositing 10x ATAC data.
If a 10x BAM is submitted, future users of the data can convert it back to FASTQ format for new analyses using the 10x tool bamtofastq.