how to get/make/find fastq file from cellranger?

Question

[B- for bioinformatics]

Hi

I need to get .fastq files from cellranger (scRNAseq).

I have checked folders, could not find fasta r fastq files, expect matrix files, how can I generate fastq with cellranger?

[ATpoint]

This lacks any details. What did you do? Add code and background information please. Do you start from fastq or BCL? What are your commands? Did you do a scRNA-seq experiment or did you download data?

Answer 1

[GenoMax]

If you only have 10x alignment and count files you can use bam2fastq utility from 10x genomics to recover fastq files.