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


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Timestamp:
Jan 18, 2021 3:35:30 PM (10 months ago)
Author:
fuji
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  • cypress/Cellranger-ARC

    v1 v1  
     1= Run Cellranger-ARC on Cypress =
     2See [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.
     3
     4Example SLURM script:
     5{{{
     6#!/bin/bash
     7#SBATCH --qos=normal            # Quality of Service
     8#SBATCH --job-name=mkFASTQ # Job Name
     9#SBATCH --time=24:00:00 # WallTime
     10#SBATCH --nodes=1               # Number of Nodes = 1
     11#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces) = 1
     12#SBATCH --cpus-per-task=1       # Number of processors per task OpenMP threads() = 1
     13#SBATCH --gres=mic:0            # Number of Co-Processors
     14#SBATCH --export=ALL
     15#SBATCH --mail-type=ALL
     16#SBATCH --mail-user='USERID'@tulane.edu # SET YOUR EMAIL ADDRESS
     17
     18module load cellranger-arc/1.0.1
     19
     20cellranger-arc mkfastq --id=tiny-bcl-atac \
     21                 --run=./cellranger-arc-tiny-bcl-atac-1.0.0 \
     22                 --csv=./cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv \
     23                 --jobmode=slurm \
     24                 --localmem=120 \
     25                 --localcores=20 \
     26                 --maxjobs=4 \
     27                 --jobinterval=1000
     28}}}
     29With this script, 'cellranger-arc' submits at most 4 sub-jobs. You can set the maximum number of jobs by changing:
     30
     31{{{
     32                 --maxjobs=18 \
     33}}}