Question about a public scRNA dataset(single end)?

Question

[soda]

When I downloaded a public scRNA dataset(SRX8492075) from the article 'Molecular architecture of the developing mouse brain', why the layout is 'single'?

Anyway, I downloaded it.Then fasterq-dump, I only got one fastq file.

enter link description here

Could one fastq file run the cellranger pipeline?

[skgtjzw]

Hey,

I am also doing this bamtofastq to convert the bam files to fastq file due to the SRA files problem. So, after the bamtofastq, I also have something like what you had:

bamtofastq_S1_L001_I1_001.fastq.gz
bamtofastq_S1_L001_I1_002.fastq.gz
bamtofastq_S1_L001_I1_003.fastq.gz
bamtofastq_S1_L001_R1_001.fastq.gz
bamtofastq_S1_L001_R1_002.fastq.gz
bamtofastq_S1_L001_R1_003.fastq.gz
bamtofastq_S1_L001_R2_001.fastq.gz
bamtofastq_S1_L001_R2_002.fastq.gz
bamtofastq_S1_L001_R2_003.fastq.gz
bamtofastq_S1_L001_R3_001.fastq.gz
bamtofastq_S1_L001_R3_002.fastq.gz
bamtofastq_S1_L001_R3_003.fastq.gz

My question is that if my data is pair end and I ran cellranger on all of these files, and it is errors free using cellranger, can I be sure I did everything correctly with this? based on your SRR number, I also have a feeling that I am using the same dataset as you did.

Best Wishes,
David

[GenoMax]

Yes you would know if cellranger analysis completes properly. There will be a nice html stats file produced if all goes well.

Answer 1

[soda]

I solved this problem with the help from a Senior Scientist(10x Genomics). Thanks a lot!

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The senior scientist said:' Since many of the public archives like SRA do not accept FASTQ files from our version 1 chemistry because the barcode is on an index read, you can download the bam file in SRA directly and convert the bam to fastq.'

1.Get the bam file in SRA

1. Convert the bam file to fastq Download 10x bamtofastq from here and use the following command line to convert bam to fastq.

   bamtofastq --nthreads=16 inputbam outputfile

After conversion, you can get I1, R1, R2, and R3. like this:

Then you can go next.