Question

How to analyze mars-seq single end-read scRNAseq data?

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18 months ago

Alex ▴ 20

I am new to cellranger and mapping. I want to analyze a SRR2319344 scRNA-seq data which only has single-end read. But cellranger count requires paired end reads (R1 R2). May I ask how to analyze this SRA data? Thanks

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cellranger single-end scRNAseq • 531 views

ADD COMMENT • link updated 18 months ago by ATpoint 85k • written 18 months ago by Alex ▴ 20

score 2 · Accepted Answer · 2023-05-17

CellRanger is specific to the 10x Chromium technologies. You cannot use it here. Do you really need to process the data from scratch? This dataset (Paul et al) is included in the Bioconductor package scRNAseq. You can download the count tables via scRNAseq::PaulHSCData(). I used this dataset via this package for my own work before, it is fine.

See for more info: https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html