Changes between Initial Version and Version 1 of cypress/Cellranger-ARC

Timestamp:

01/18/21 15:35:30 (3 years ago)

Author:

fuji

Comment:

—

cypress/Cellranger-ARC

@@ +1 @@
+= Run Cellranger-ARC on Cypress =
+See [https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/mkfastq Generating FASTQs with cellranger-arc mkfastq]. This page to show how to run Cellranger-ARC with [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/cluster-mode the cluster mode] on Cypress.
+
+Example SLURM script:
+{{{
+#!/bin/bash
+#SBATCH --qos=normal            # Quality of Service
+#SBATCH --job-name=mkFASTQ # Job Name
+#SBATCH --time=24:00:00 # WallTime
+#SBATCH --nodes=1               # Number of Nodes = 1
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces) = 1
+#SBATCH --cpus-per-task=1       # Number of processors per task OpenMP threads() = 1 
+#SBATCH --gres=mic:0            # Number of Co-Processors
+#SBATCH --export=ALL
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user='USERID'@tulane.edu # SET YOUR EMAIL ADDRESS
+
+module load cellranger-arc/1.0.1
+
+cellranger-arc mkfastq --id=tiny-bcl-atac \
+                 --run=./cellranger-arc-tiny-bcl-atac-1.0.0 \
+                 --csv=./cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv \
+                 --jobmode=slurm \
+                 --localmem=120 \
+                 --localcores=20 \
+                 --maxjobs=4 \
+                 --jobinterval=1000
+}}}
+With this script, 'cellranger-arc' submits at most 4 sub-jobs. You can set the maximum number of jobs by changing:
+
+{{{
+                 --maxjobs=18 \
+}}}