CellRanger-ATAC-Sapelo2 - Revision history

Shtsai at 00:21, 5 April 2026

2026-04-05T00:21:36Z

← Older revision		Revision as of 20:21, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	2.1.0		2.1.0

	=== Author / Distributor ===		== Author / Distributor ==

	Please see https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac		Please see https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac

	=== Description ===		== 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."		"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		More details are at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac

	=== Running Program ===		== Running Program ==

	* Version 2.1.0 is installed at /apps/eb/CellRanger-ATAC/2.1.0		* Version 2.1.0 is installed at /apps/eb/CellRanger-ATAC/2.1.0
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Source code is download from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest		Source code is download from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea: /* Version */

2024-05-09T14:45:19Z

Version

← Older revision		Revision as of 10:45, 9 May 2024
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	=== Version ===		=== Version ===
	1.2.~~0, 2.0~~.0		2.1.0

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	* ~~version 1.~~2.~~0 is installed at /apps/eb/CellRanger-ATAC/~~1~~.2.0~~		* Version 2.1.0 is installed at /apps/eb/CellRanger-ATAC/2.1.0
	* 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		To use version 2.1.0, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml CellRanger-ATAC/1.2.0		ml CellRanger-ATAC/2.1.0
	</pre>		</pre>

	~~To use version 2.0.0, please load the module with~~		Here is an example of a shell script, sub.sh, to run on the batch queue:<div class="gscript2">
	~~<pre class="gscript">~~
	~~ml CellRanger-ATAC/2.0.0~~
	~~</pre>~~

	Here is an example of a shell script, sub.sh, to run on the batch queue:

	<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br>
	<nowiki>#</nowiki>SBATCH --job-name=j_cellranger-atac<br>		<nowiki>#</nowiki>SBATCH --job-name=j_cellranger-atac<br>
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml CellRanger-ATAC/1.2.0<br>		ml CellRanger-ATAC/2.1.0<br>
	cellranger-atac count --localcores=<u>8</u> <u>[options]</u><br>		cellranger-atac count --localcores=<u>8</u> <u>[options]</u><br>
	</div>		</div>

Moses at 20:21, 5 May 2021

2021-05-05T20:21:15Z

← Older revision		Revision as of 16:21, 5 May 2021
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	=== Installation ===		=== Installation ===

	Source code is ~~obtained~~ from ~~[http~~://~~bowtie-bio~~.~~sourceforge~~.~~net~~/~~bowtie2~~/~~index.shtml Bowtie2]~~		Source code is download from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Moses at 20:11, 5 May 2021

2021-05-05T20:11:11Z

← Older revision		Revision as of 16:11, 5 May 2021
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	In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.		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 ~~refer to Running_Jobs_on_the_sapelo2_cluster, Run X window Jobs~~ and ~~Run interactive Jobs for more details of running jobs at Sapelo2 cluster~~.		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:		Here is an example of job submission command:

Moses at 20:08, 5 May 2021

2021-05-05T20:08:02Z

← Older revision		Revision as of 16:08, 5 May 2021
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml CellRanger-ATAC/1.2.0<br>		ml CellRanger-ATAC/1.2.0<br>
	cellranger-atac count --localcores=<u>8</u> <u>[options]</u><br>		cellranger-atac count --localcores=<u>8</u> <u>[options]</u><br>
	</div>		</div>

			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 refer to Running_Jobs_on_the_sapelo2_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Sapelo2 cluster.

	Here is an example of job submission command:		Here is an example of job submission command:

Moses at 20:06, 5 May 2021

2021-05-05T20:06:12Z

← Older revision		Revision as of 16:06, 5 May 2021
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	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --ntasks=1<br>		<nowiki>#</nowiki>SBATCH --ntasks=1<br>
	<nowiki>#</nowiki>SBATCH --cpus-per-task=8<br>		<nowiki>#</nowiki>SBATCH --cpus-per-task=<u>8</u><br>
	<nowiki>#</nowiki>SBATCH --constraint=EDR		<nowiki>#</nowiki>SBATCH --constraint=EDR<br>
	<nowiki>#</nowiki>SBATCH --mem=<u>32gb</u><br>		<nowiki>#</nowiki>SBATCH --mem=<u>32gb</u><br>
	<nowiki>#</nowiki>SBATCH --time=<u>120:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>120:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=log.%j.out<br>		<nowiki>#</nowiki>SBATCH --output=log.%j.out<br>
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml CellRanger-ATAC/1.2.0<br>		ml CellRanger-ATAC/1.2.0<br>
	cellranger-atac count --localcores=8 <u>[options]</u><br>		cellranger-atac count --localcores=<u>8</u> <u>[options]</u><br>
	</div>		</div>

Moses at 20:05, 5 May 2021

2021-05-05T20:05:22Z

← Older revision		Revision as of 16:05, 5 May 2021
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	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --ntasks=1<br>		<nowiki>#</nowiki>SBATCH --ntasks=1<br>
	<nowiki>#</nowiki>SBATCH --cpus-per-task=8		<nowiki>#</nowiki>SBATCH --cpus-per-task=8<br>
	<nowiki>#</nowiki>SBATCH --constraint=EDR		<nowiki>#</nowiki>SBATCH --constraint=EDR
	<nowiki>#</nowiki>SBATCH --mem=<u>32gb</u><br>		<nowiki>#</nowiki>SBATCH --mem=<u>32gb</u><br>

Moses at 20:05, 5 May 2021

2021-05-05T20:05:03Z

← Older revision		Revision as of 16:05, 5 May 2021
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	<nowiki>#</nowiki>SBATCH --job-name=j_cellranger-atac<br>		<nowiki>#</nowiki>SBATCH --job-name=j_cellranger-atac<br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --partition=batch<br>
	<nowiki>#</nowiki>SBATCH --ntasks=~~<u>~~1~~</u>~~<br>		<nowiki>#</nowiki>SBATCH --ntasks=1<br>
	<nowiki>#</nowiki>SBATCH --cpus-per-task=8		<nowiki>#</nowiki>SBATCH --cpus-per-task=8
	<nowiki>#</nowiki>SBATCH --constraint=EDR		<nowiki>#</nowiki>SBATCH --constraint=EDR

Moses: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.0, 2.0.0 === Author /..."

2021-05-05T20:04:24Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.0, 2.0.0 === Author /..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== 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
<pre class="gscript">
ml CellRanger-ATAC/1.2.0
</pre>

To use version 2.0.0, please load the module with
<pre class="gscript">
ml CellRanger-ATAC/2.0.0
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_cellranger-atac 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=8
<nowiki>#</nowiki>SBATCH --constraint=EDR
<nowiki>#</nowiki>SBATCH --mem=32gb 
<nowiki>#</nowiki>SBATCH --time=120:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 
ml CellRanger-ATAC/1.2.0 
cellranger-atac count --localcores=8 [options] 
</div>

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
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

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== System ===
64-bit Linux