Visium analysis pipeline
The general gene expression analysis pipeline of 10X Visium data
Usage
- Prepare a sample table file (tab-delimited). sample.tsv must have columns of id, fastqs, image, slide, area with a header line.
example (sample.tsv):
id | fastqs | image | slide | area |
---|---|---|---|---|
CRC_16 | /archive/PCDC/PCDC_Core/shared/pipelines/projects/CRC_OSCC_visium/fastq/CRC_16 | /archive/PCDC/PCDC_Core/shared/pipelines/projects/CRC_OSCC_visium/tiff/CRC_16.tiff | V10S15-020 | D1 |
OSCC_2 | /archive/PCDC/PCDC_Core/shared/pipelines/projects/CRC_OSCC_visium/fastq/OSCC_2 | /archive/PCDC/PCDC_Core/shared/pipelines/projects/CRC_OSCC_visium/tiff/OSCC_2.tiff | V11A07-022 | A1 |
- Create an analysis script named "run.sh"
perl generate_scripts.pl sample.tsv
- Submit the analysis job to Slurm scheduler.
perl sbatch.pl -p 256GBv1 run.sh
generate_scripts.pl
Usage: perl generate_scripts.pl [options] sample.tsv
Options: -h display this help message
-p INT number of CPU threads [32]
-m INT memory limit (GB) [240]
-r DIR transcriptome reference path [/archive/PCDC/PCDC_Core/shared/pipelines/data/10xgenomics/supp/spatial-exp/refdata-gex-GRCh38-2020-A]
-n INT minimum UMI count per spot [100]
-P FILE pathway-to-gene file [/archive/PCDC/PCDC_Core/shared/pipelines/projects/NGS_scripts/visium/human.pathway.gene.txt]
sample.tsv must have columns of id, fastqs, image, slide, area with a header line.
seurat_spatial.spatial_plot_gene.R
example:
Rscript seurat_spatial.spatial_plot_gene.R seurat_spatial.RData spatial_plot_gene.pdf 8 8 ACTB TP53