I need to generate count matrix from raw FASTQ files sequenced on 10X genomics. Can you please give me an overview ?
Thanks in advance
What's wrong with cellranger?
Generally scRNA-seq fastq files are processed with Cell Ranger (10X), STARsolo, alevin-fry (Salmon), or kallisto bustools. I personally recommend either Cell Ranger or alevin-fry.
Thanks Castro. The CellRanger is free and can be downloaded in linux/ubuntu ? Is that right ?
they’re all unix freeware. be sure to spend time going through tutorials and get a background first.
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