Question: I want to upload my 10x Genomics data to NCBI GEO. What file(s) should I upload?
Answer: For uploading 10x Genomics data to GEO, submitters should either upload FASTQ files (both barcode reads and transcript/feature reads) or 10x BAM files. GEO will then submit the uploaded data files to the Sequence Read Archive (SRA)on your behalf.
If available, SRA encourages the submission of the 10x BAM file (possorted_genome_bam.bam) in addition to the FASTQ files. 10x Genomics offer a tool called bamtofastq for converting 10x BAMs back to FASTQ files that can be used as inputs to re-run the analysis. In addition, SRA pipeline detects 10X BAM files and makes the originally submitted file available from the Download tab of the Run Browser. Also please note that for Single Cell ATAC application, it is strongly recommended to only submit 10x BAM file.