From feef36b545d85127cb68ea26de671d8c58ec4caa Mon Sep 17 00:00:00 2001 From: Elizabeth Partan Date: Wed, 22 Apr 2026 13:49:25 -0400 Subject: [PATCH] Update pre-process-w-cellranger.md for CellRanger 9.0 --- pre-process-w-cellranger.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/pre-process-w-cellranger.md b/pre-process-w-cellranger.md index e69451f..7257286 100644 --- a/pre-process-w-cellranger.md +++ b/pre-process-w-cellranger.md @@ -18,7 +18,7 @@ Here are the steps that need to be completed prior to running cellranger. #### I have mouse or human -We have prebuilt references for mouse and human located here: +There are prebuilt references for mouse and human located on O2. For the paths, run `module spider cellranger`. #### I have another genome @@ -37,7 +37,7 @@ Below is an example script for a non-model reference #SBATCH -c 1 #SBATCH --mem=48G -module load cellranger/7.1.0 +module load cellranger/9.1.0 cellranger mkref \ --genome=my_nonmodel_genome \ @@ -117,8 +117,8 @@ Here is an example sbatch script for running cellranger as an array ```(bash) #!/bin/bash -#SBATCH --job-name=CellRangerCount3 # Job name -#SBATCH --partition=short # Partition name +#SBATCH --job-name=CellRangerCount # Job name +#SBATCH --partition=short # Partition name #SBATCH --time=0-05:00 # Runtime in D-HH:MM format #SBATCH --nodes=1 # Number of nodes (keep at 1) #SBATCH --ntasks=1 # Number of tasks per node (keep at 1) @@ -128,14 +128,15 @@ Here is an example sbatch script for running cellranger as an array #SBATCH --output=jobid_%j.out # File to which STDOUT will be written, including job ID -samp=$(awk -v awkvar="${SLURM_ARRAY_TASK_ID}" 'NR==awkvar' samples.txt) ### This line will take the numeric slurm array task id and find the corresponding line number in samples.txt. The sample name is made into a variable called samp. +samp=$(awk -v awkvar="${SLURM_ARRAY_TASK_ID}" 'NR==awkvar' samples.txt) ### This line will take the numeric slurm array task id and find the corresponding line number in samples.txt. The sample name is made into a variable called samp. This is also what your output folders will be called. -module load cellranger/7.1.0 +module load cellranger/9.1.0 cellranger count \ - --id=${samp} \ ## This is what your output folders will be named + --id=${samp} \ --fastqs=/path/to/your/folder/of/fastq/folders/${samp} \ --transcriptome=/path/to/your/genome \ + --create-bam=false \ --localcores=16 \ --localmem=128