Merge pull request #2 from claraliu97/main

Adding sn processing scripts

Processing_script/cellranger-arc.v.2.0.0.sh

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+#Basic commands to run cellranger for single-nuclei Multiome-sequencing Data
+
+#References: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
+
+#Reference Genome:https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest?
+
+#Sample_ID
+sample=''
+
+#Path to reference
+reference='refdata-cellranger-arc-GRCh38-2020-A-2.0.0'
+
+#Path to libraries
+libraries='library.csv'
+
+cellranger-arc-2.0.0/cellranger-arc count --id $sample --reference  $reference --libraries $libraries --disable-ui --localcores 12 --localmem 100

Processing_script/cellranger.v5.0.1.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 --localmem=300 --localcores=40 --transcriptome $reference