In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?
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5 weeks ago
mrj ▴ 70

In single cell RNA-seq, do we perform regular quality checks and adapter trimming (just like in regular RNA-seq) before using cellranger?

cellranger adapter_trimming QC scRNA-seq • 433 views
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5 weeks ago
colindaven ★ 3.3k

No. Indeed, you can't do it, because CellRanger takes a runfolder, not FASTQ files, as the default input and performs the demultiplexing itself.

Of course, you can demux yourself and run QC on a big unassigned FASTQ, which might help if the run was very suboptimal, but in general the stats from and post CellRanger are what you want.

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