how to get/make/find fastq file from cellranger?
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17 months ago

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?

RNA-Seq rna-seq • 350 views
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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?

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17 months ago
GenoMax 104k

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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