Added spaceranger v1.3 and rotate-images parameter

Processing_script/spaceranger.v1.3.sh

@@ -0,0 +1,52 @@
+#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"
+--reorient-images \
+--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"
+--reorient-images \
+--localcores=32 \
+--localmem=150
+

Processing_script/spaceranger.v2.1.1.sh

@@ -1,4 +1,6 @@
 #Basic commands to run Space ranger for spatial transcriptomics Data
+# Note, both v2.0 and v2.1.1 uses the same script snippet
+
 
 #References: https://www.10xgenomics.com/support/software/space-ranger
 
@@ -32,6 +34,7 @@ mkdir -p $output_folder && cd $output_folder && spaceranger count --id="$sample"
 --image="PATH/TO/HE_IMAGE_FILE.tif" \
 --slide="SLIDE_ID" \ # e.g. "V12U06-375"
 --area="AREA_ID" \ # e.g. "B1"
+--reorient-images true \
 --localcores=32 \
 --localmem=150
 
@@ -45,6 +48,7 @@ mkdir -p $output_folder && cd $output_folder && spaceranger count --id="$sample"
 --image="PATH/TO/HE_IMAGE_FILE.tif" \
 --slide="SLIDE_ID" \ # e.g. "V12U06-375"
 --area="AREA_ID" \ # e.g. "B1"
+--reorient-images true \
 --localcores=32 \
 --localmem=150