Processing scripts

Processing_script/cellranger.v6.0.2.sh

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+#Basic commands to run cellranger for single-cell or single-nuclei RNA-sequencing Data
+
+#References: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
+
+#Reference Genome: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
+
+#Sample_ID
+sample=''
+
+#Path to reference
+reference='refdata-gex-GRCh38-2020-A'
+
+#Path to FASTQ files
+fastq_dir='FASTQ/'
+
+
+cellranger-6.0.2/cellranger count --id $sample --fastqs $fastq_dir --include-introns --localmem=120 --localcores=16 --transcriptome $reference

Processing_script/spaceranger.v2.1.1.sh

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+#Basic commands to run Space ranger for spatial transcriptomics Data
+
+#References: https://www.10xgenomics.com/support/software/space-ranger
+
+#Reference Genome: https://www.10xgenomics.com/support/software/space-ranger/downloads#reference-downloads
+
+#Sample_ID
+sample=''
+
+#Path to reference
+reference='refdata-gex-GRCh38-2020-A'
+
+# Probe set (FFPE): Human Probe Set v1
+# Available at 10x Genomics website: https://www.10xgenomics.com/support/spatial-gene-expression-ffpe/documentation/workflows/cytassist-ffpe/steps/probe-sets/visium-ffpe-probe-sets-overview
+Probe_set_file = "PATH/TO/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv"
+
+#Path to FASTQ files
+fastq_dir='PATH/TO/FASTQ/'
+
+# Path to output
+output_folder="SPACERANGE_OUTPUT/FOLDER/${sample}"
+
+# (Optional) in terms of sample with manual alignment
+# Add 
+# --loupe-alignment="PATH/TO/SAMPLE_manual_alignment.json" \
+
+# OCT version
+mkdir -p $output_folder && cd $output_folder && spaceranger count --id="$sample" \
+--sample="$sample" \
+--transcriptome="$reference" \
+--fastqs="$fastq_dir" \
+--image="PATH/TO/HE_IMAGE_FILE.tif" \
+--slide="SLIDE_ID" \ # e.g. "V12U06-375"
+--area="AREA_ID" \ # e.g. "B1"
+--localcores=32 \
+--localmem=150
+
+
+# FFPE version
+mkdir -p $output_folder && cd $output_folder && spaceranger count --id="$sample" \
+--sample="$sample" \
+--transcriptome="$reference" \
+--probe-set="$Probe_set_file" \
+--fastqs="$fastq_dir" \
+--image="PATH/TO/HE_IMAGE_FILE.tif" \
+--slide="SLIDE_ID" \ # e.g. "V12U06-375"
+--area="AREA_ID" \ # e.g. "B1"
+--localcores=32 \
+--localmem=150
+