Question: Why do I not see or see incomplete fastqs for the SRA of my interest ? How can I get the fastqs ?
Answer: Sometimes, the 10x fastqs are not uploaded to the public repositories such as SRA. Instead, customers upload the bam file which is one of the output files generated by Cell Ranger. If present, the bams may be found as separate links in the "Data access" tab of the SRA.
For example, for the SRA: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5643130, the bam file can be found here in the "Original format" section highlighted below.
You can download the bam file and then convert it to fastq using a 10x utility tool called bamtofastq described here.