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SCRNA analysis

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
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updated by ATpoint ATpoint • written by shivangi.agarwal800 shivangi.agarwal800

What's wrong with cellranger?

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written by swbarnes2 swbarnes2

1 answer

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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written by rpolicastro rpolicastro

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

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written by shivangi.agarwal800 shivangi.agarwal800

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

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written by ATpoint ATpoint

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