Space Ranger count

Spatial GEX

# Pipeline for fresh frozen (FF) tissue section
# Fastq name must be: sample_S1_L00[lane_number]_[I1/R1/R2]_001.fastq.gz
spaceranger count \
--sample=sampleName \
--fastqs=/opt/data \
--image=/opt/data/test.tif \
--id=out \
--transcriptome=/opt/cellranger/refdata-gex-GRCh38-2020-A \
--slide=V19L01-041 \
--area=A1

*流程参考资料: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/choosing-pipelines

CytAssist GEX

spaceranger count \
--id=out \
--transcriptome=/opt/cellranger/refdata-gex-GRCh38-2020-A \
--probe-set=/opt/spaceranger-2.0.0/probe_set/Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv \
--fastqs=/opt/data \
--sample=sample \
--cytaimage=/opt/data/sample.tif \
--image=/opt/data/sample_bright.tif \
--slide=V49J01-123 \
--area=A1 \
--localcores=8 \
--localmem=64

*参考资料: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/probe-based-assay-count-cytassist-gex

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Space Ranger下载: https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest