I am trying to download a single cell RNAseq run from NCBI. It is SRR7898910 also found here
I try to download the data using the NCBI recommended way of downloading the SRA file using prefetch and the using the following command on the terminal:
fastq-dump --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --split-2 --clip SRR7898910
My issue is that this creates a single fastq file - that is 16GB. So I assume it is all the sequences of all the cells in one fastq file. Does anyone know how to get 2 fastq files (forward and reverse) for each cell in the study? It seems like the logical first step as I want to realign them and analyse them in house. Or if that is not possible then to get a bam file for each cell for counting.
Thanks for any recommendations you may have. best wishes