From fa7b74783586945a7d9efefaece256bb00fb6273 Mon Sep 17 00:00:00 2001 From: "Jingxian (Clara) Liu" Date: Thu, 27 Jun 2024 15:42:56 -0500 Subject: [PATCH] Adding sn processing scripts --- Processing_script/cellranger-arc.v.2.0.0.sh | 16 ++++++++++++++++ Processing_script/cellranger.v5.0.1.sh | 17 +++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 Processing_script/cellranger-arc.v.2.0.0.sh create mode 100644 Processing_script/cellranger.v5.0.1.sh diff --git a/Processing_script/cellranger-arc.v.2.0.0.sh b/Processing_script/cellranger-arc.v.2.0.0.sh new file mode 100644 index 0000000..a69781c --- /dev/null +++ b/Processing_script/cellranger-arc.v.2.0.0.sh @@ -0,0 +1,16 @@ +#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 diff --git a/Processing_script/cellranger.v5.0.1.sh b/Processing_script/cellranger.v5.0.1.sh new file mode 100644 index 0000000..d3b72a7 --- /dev/null +++ b/Processing_script/cellranger.v5.0.1.sh @@ -0,0 +1,17 @@ +#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