Public single cell rna-seq with only one fastq file. How can I handle it?

Question

[기석]

Hello

I greatly thank you to all of you in this website.

I downloaded four of samples from PRJNA606815( https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP249907&o=acc_s%3Aa ), using fasterq-dump.

The data are single-cell rna seq with 3' chemistry 10x genomics but I have one fastq file per sample.

I expected some fastq files per sample but failed.

Does anyone know how to handle it in this situation?

Answer 1

[GenoMax]

If you go to the Data access tab of the SRA entries for these samples you can find the original BAM files submitted: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR11106929&display=data-access

Use bamtofastq (LINK) utility provided by 10x to re-create the correct R1,R2,I1 files.

[기석]

I really appreciate your comment yir.