I am trying to download data from SRA using fastq-dump. The data I am trying to download is from SRR10349891. The sequencing design is 10x Genomics V2, and the layout is Paired. Based on some of the tutorials from cellranger (https://bioinformaticsworkbook.org/dataAnalysis/RNA-Seq/Single_Cell_RNAseq/Chromium_Cell_Ranger.html) I would expect the command:
fastq-dump --split-files SRR10349891
to yield two files SRR10349891_1.fastq and SRR10349891_2.fastq.
However, I only get one file (SRR10349891.fastq). All of the online resources I have seen require both .fastq files from this process in order to analyze this type of data (using methods like scPipe). Is there only file available for download from this experiment?
If so, are there any methods for converting this single .fastq file to two files (one containing the transcripts, and one containing the barcodes/umi)?
The other option that I have thought about is downloading the available .bam files for this experiment, and then using the 10X genomics bamtofastq tool to convert these back to fastq files.