how to get/make/find fastq file from cellranger?
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?
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GenoMax
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B- for bioinformatics •
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B- for bioinformatics •
1 answer
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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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?