Question

SCRNA analysis

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2.4 years ago

shivangi.agarwal800 ▴ 120

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 • 1.2k views

ADD COMMENT • link updated 2.4 years ago by ATpoint 85k • written 2.4 years ago by shivangi.agarwal800 ▴ 120

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What's wrong with cellranger?

ADD REPLY • link 2.4 years ago by swbarnes2 14k

score 1 · Answer 1 · 2022-07-02

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2.4 years ago

rpolicastro 13k

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.

ADD COMMENT • link 2.4 years ago by rpolicastro 13k

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

ADD REPLY • link 2.4 years ago by shivangi.agarwal800 ▴ 120

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

ADD REPLY • link 2.4 years ago by ATpoint 85k