I have been trying to download the fastq files of a single cell RNA experiment from SRX8632237 with the following SRA runs :
The runs show that it has 3 reads per spot (link). However, I am unable to download the three fastq files separately using sra-tookit (2.10.7). I always get one file.
I have tried multiple combination of fasterq-dump and fastq-dump to download the samples and used the options --split-files, --split-spot, --split-e, --split-3, --concatenate reads, --include-technical, --skip-technical, with prefetch, without prefetch and none of the combinations splits the files according to the reads.
Could someone please help me resolve this problem and let me know where I might be going wrong?
Kevin's command above worked for me as well, either prefetch or not. How about installing the latest version of the SRA tool kit instead of Version 2.10.7? Version 2.11.1 is available now. Also, I don't think you need to download data through AWS in this case. The data storage issues for the free account caused me to panic...