Skip to content
Snippets Groups Projects
user avatar
Jiwoong Kim authored
1dd996a4

Visium analysis pipeline

The general gene expression analysis pipeline of 10X Visium data

Usage

  1. 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
  1. Create an analysis script named "run.sh"
perl generate_scripts.pl sample.tsv
  1. 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