paired fastq file

Question

[Andy]

Hello everyone,

I am hoping you could help me with a problem to deal with single fastq file. I am trying to download the fastq file for study GSM5467406. Although this is a paired end, but only one fastq file available. I am wonder what should I do about this one. Since I hope I could re-run the cell ranger process. Because I use different version of cell ranger with this study.

Answer 1

[MolGeek]

Hi, you can download the SRA files from https://www.ncbi.nlm.nih.gov/sra?term=SRX11523859 and then run:

fasterq-dump SRR15217901

This should produce 2 fastq files for each replicate.

[Andy]

thank you so much. I wonder how to download the fastq-dump tool?

[MolGeek]

Its a part of the sra toolkit. https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

Answer 2

[GenoMax]

These are 10x dataset so you are going to get three files from this data by doing (this is the fastq-dump program not fasterq-dump mentioned in other answer)

$ fastq-dump --split-files -F SRR15217901

_1 file = Illumina index
_2 file = Cellbarcode+UMI
_3 file = actual RNA read.

You will have to rename these files in a certain way if you want to use them with cellranger --> How to rename fastqs for cell ranger ?