I am trying to get the fastq files for the dataset with GEO number GSE122960. Unfortunately, fftp links for such files are not available (I could only find links to an SRA formatted fastq which I cannot use). So I decided to use fastq-dump...
I did the following:
fastq-dump --split-files --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --clip --defline-seq '@$ac.$si.$sg/$ri' --defline-qual '+' /content/SRR8085151 -I
However, fastq-dump returns a single fastq, instead of two fastqs as specified by --split-files. What am I doing wrong? The resulting file name is SRR8085151_pass_1.fastq.gz
Thanks so much!!!