I am hoping you could help me with a problem to deal with single fastq file. I am trying to download the fastq file for study GSM5467406. Although this is a paired end, but only one fastq file available. I am wonder what should I do about this one. Since I hope I could re-run the cell ranger process. Because I use different version of cell ranger with this study.
These are 10x dataset so you are going to get three files from this data by doing (this is the fastq-dump program not fasterq-dump mentioned in other answer)
$ fastq-dump --split-files -F SRR15217901
_1 file = Illumina index _2 file = Cellbarcode+UMI _3 file = actual RNA read.
thank you so much. I wonder how to download the fastq-dump tool?
Its a part of the sra toolkit. https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit