How to perform sequence quality filtering of raw reads for single cell RNA seq?

How to perform sequence quality filtering of raw reads for single cell RNA seq?

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I have a few single-cell RNA-seq samples (raw fastq reads). When I process raw reads, what should I do first?
Is it demultiplexing? If so, what is the best tool I can use? Can I use cellranger for that?
Most tutorials I read talk about analysis after the alignment.

Thank you in advance.


QC


raw_reads


cellranger


scRNA-seq


UMI

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2 hours ago by


mrj

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