Why there are only two .fastq files in scATAC-seq raw data?

Question

[浩然]

I am new for single cell data analysing. I use the sra-tool and download the .sra data from https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA532774, and I specifically down the SRR8893771 with command prefetch SRR8893771. And I then I call fastq-dump to generate the .fastq files, but I however obtained only two .fastq files SRR8893744_1.fastq and SRR8893744_2.fastq. And I know there should be four (I1, R1, R2, R3) for cellranger-atac. I therefore am confused and I don't know whether I processed in a wrong way or the data only contains two files.

Answer 1

[ATpoint]

I would ignore the fastq submission of NCBI for 10x data when possible. Look at https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR8893737&display=data-access which indicates that the 10x bam file has been uploaded. Download this and convert back to fastq with the 10x application bam2fastq. It's hosted at aws s3, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-aws-download/