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