CellRanger-ATAC-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
1.2.0, 2.0.0
Author / Distributor
Please see https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
Description
"Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. Cell Ranger ATAC includes four pipelines relevant to single cell chromatin accessibility experiments." More details are at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
Running Program
- version 1.2.0 is installed at /apps/eb/CellRanger-ATAC/1.2.0
- Version 2.0.0 is installed at /apps/eb/CellRanger-ATAC/2.0.0
To use version 1.0.0, please load the module with
ml CellRanger-ATAC/1.2.0
To use version 2.0.0, please load the module with
ml CellRanger-ATAC/2.0.0
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_cellranger-atac
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --constraint=EDR
#SBATCH --mem=32gb
#SBATCH --time=120:00:00
#SBATCH --output=log.%j.out
#SBATCH --error=log.%j.err
#SBATCH --mail-user=username@uga.edu
#SBATCH --mail-type=ALL
cd $SLURM_SUBMIT_DIR
ml CellRanger-ATAC/1.2.0
cellranger-atac count --localcores=8 [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please use --constraint=EDR header in your job submission script for a quicker job start time and optimal job performance.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml CellRanger-ATAC/1.2.0
cellranger-atac -h
cellranger-atac -h (1.2.0)
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
-------------------------------------------------------------------------------
Usage:
cellranger-atac mkfastq
cellranger-atac count
cellranger-atac aggr
cellranger-atac reanalyze
cellranger-atac mkref
cellranger-atac testrun
cellranger-atac upload
cellranger-atac sitecheck
cellranger-atac count -h
cellranger-atac count (1.2.0)
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
-------------------------------------------------------------------------------
The commands below should be preceded by 'cellranger-atac':
Usage:
count
--id=ID
--fastqs=PATH
[--sample=PREFIX]
[options]
count <run_id> <mro> [options]
count -h | --help | --version
Arguments:
id A unique run id, used to name output folder [a-zA-Z0-9_-]+.
fastqs Path of folder created by mkfastq or bcl2fastq.
sample Prefix of the filenames of FASTQs to select.
Options:
# Sample Specification
--reference=PATH Path of folder containing a 10x-compatible reference.
Required.
--description=TEXT More detailed sample description. Optional.
--lanes=NUMS Comma-separated lane numbers.
--indices=INDICES Deprecated. Not needed with the output of
cellranger-atac mkfastq, or bcl2fastq
--project=TEXT Name of the project folder within a mkfastq or
bcl2fastq-generated folder to pick FASTQs from.
# ATAC analysis
--force-cells=N Define the top N barcodes with the most reads as
cells. N must be a positive integer <=
20,000. Please consult the documentation
before using this option. Optional.
--dim-reduce=MODE Dimensionality reduction mode for clustering: 'lsa'
(default), 'plsa', or 'pca'. Optional.
# Downsampling
--downsample=GB Downsample input FASTQs to approximately GB
gigabases of input sequence. Optional.
# Martian Runtime
--jobmode=MODE Job manager to use. Valid options:
local (default), sge, lsf, or a .template file
--localcores=NUM Set max cores the pipeline may request at one time.
Only applies to local jobs.
--localmem=NUM Set max GB the pipeline may request at one time.
Only applies to local jobs.
--localvmem=NUM Set max virtual address space in GB for the pipeline.
Only applies to local jobs.
--mempercore=NUM Reserve enough threads for each job to ensure enough
memory will be available, assuming each core on your
cluster has at least this much memory available.
Only applies in cluster jobmodes.
--maxjobs=NUM Set max jobs submitted to cluster at one time.
Only applies in cluster jobmodes.
--jobinterval=NUM Set delay between submitting jobs to cluster, in ms.
Only applies in cluster jobmodes.
--overrides=PATH The path to a JSON file that specifies stage-level
overrides for cores and memory. Finer-grained
than --localcores, --mempercore and --localmem.
Consult the 10x support website for an example
override file.
--uiport=PORT Serve web UI at http://localhost:PORT
--disable-ui Do not serve the UI.
--noexit Keep web UI running after pipestance completes or fails.
--nopreflight Skip preflight checks.
-h --help Show this message.
--version Show version.
Note: 'cellranger-atac count' works as follows:
set --fastqs to the folder containing FASTQ files. In addition,
set --sample to the name prefixed to the FASTQ files comprising your sample.
For example, if your FASTQs are named:
subject1_S1_L001_R1_001.fastq.gz
then set --sample=subject1
Installation
Source code is download from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
System
64-bit Linux