I would really like to download the raw data of a specific public single-cell RNA-Seq experiment (ENA, GEO). As the BCL files do not seem to be available the most "raw" format would probably be paired end fastq files. Currently I am unable to download the files in a split way and I would really appreciate your help.
For simplicity just focus on one sample: Donor1_scRNA-seq_rep1 (GSM3052917, Experiment: SRX3815586, Run: SRR6860519)
I already tried
fasterq-dump with all possible split parameters (
--split-files etc.) but despite of the parameter I just receive one fastq file.
fastq-dump --split-files SRR6860519 fasterq-dump -S SRR6860519
The library type is definitely
paired and at ENA one can see two submitted MD5-sums per sample.
Does anyone know how to split these samples correctly? And does it make a difference if I provide the experiment accession or the run accession to fastq-dump/fasterq-dump?
Thanks in advance!