fastq-dump unable to separate fastq files from scRNA-seq SRA files

Question

[ravihansa82]

Hi all,

I recently downloaded a scRNA-seq file (SRR12661516) using sratoolkit. Then I needed to get the fastq files as I plan to upload the resulting fastq files to 10X genomics cloud for a new analysis. I used fastq-dump --split-3 SRR12661516 command to get the fastq files. I expected to get 3 fastq files:

SRR12661516_S1_L001_I1_001.fastq
SRR12661516_S1_L001_R1_001.fastq
SRR12661516_S1_L001_R2_001.fastq

Unfortunately, I got a fastq file named SRR12661516_pass.fastq. Can someone explain why I get this output? Also, I would appreciate it if you could help me to get the required fastq files. Thank you

[GenoMax]

Your best bet is to download the original fastq files that were submitted. You will find those under the Data Access tab of each sample record. These files are in amazon cloud. Example below.

https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR12661516&display=data-access

Answer 1

[GenoMax]

I was able to get three expected files by doing (sra-toolkit v.3.0.1)

$ fastq-dump -F --split-files SRR12661516

$ head -4 SRR12661516*
==> SRR12661516_1.fastq <==
@NS500422:619:HM2FNBGX5:1:11101:9269:1047
GCACAATG
+NS500422:619:HM2FNBGX5:1:11101:9269:1047
AA/AAEAE

==> SRR12661516_2.fastq <==
@NS500422:619:HM2FNBGX5:1:11101:9269:1047
AAGTCNGGTAGTAGTAAAAACAGGTA
+NS500422:619:HM2FNBGX5:1:11101:9269:1047
AAAAA#EEEEEEEEEEEEEEEEEEEE

==> SRR12661516_3.fastq <==
@NS500422:619:HM2FNBGX5:1:11101:9269:1047
NACAAGTCAANTANTACAATNANATATNATACTNNTNANATGANTATTNNNAATANNN
+NS500422:619:HM2FNBGX5:1:11101:9269:1047
#AAA//////#/6#/6////#/#////#///6/##/#/#//6/#<A6/###/<</###

You will need to rename the files in the format cellranger expects (I1,R1, R2) manually.

[ravihansa82]

Hi GenoMax, Thanks for your help. I also found suggestions from this link and was able to get three files as you have also shown here. Yeah, I feel the same that I have to rename the sample according to cellranger format.

[Ram]

Accept GenoMax's answer if it solves your problem.