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Old 11-11-2019, 10:46 AM   #1
hoytpr
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Location: Stillwater

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Default Equivalent of Cellranger for BioRad ddSEQ?

We've sequenced some libraries for a client that used the BioRad ddSEQ instrument to isolate cells. We were told by Bio-Rad an "R-script" exists to substitute for the 10X Genomics cellranger first steps when we are starting after bcl2fastq. I've looked and found lots of software. Does anybody know specifically what this sales rep was talking about?

We don't have BaseSpace. It looks like we'll be using Seurat for DE analyses and visualization, but their vignettes (at least the first, easiest, ones) use 10X genomics (cellranger) outputs. Any easy ways to go from bcl2fastq outputs to Seurat without cellranger (nothing against cellranger!).

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