SCRNA analysis
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6 weeks ago

Hi Guys,

I need to generate count matrix from raw FASTQ files sequenced on 10X genomics. Can you please give me an overview ?

Thanks in advance

single cell • 448 views
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What's wrong with cellranger?

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6 weeks ago

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.

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Thanks Castro. The CellRanger is free and can be downloaded in linux/ubuntu ? Is that right ?

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they’re all unix freeware. be sure to spend time going through tutorials and get a background first.

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