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<pre><code>./scMaestro atac -h
usage: scMaestro atac [-h] -f [FASTQPATH [FASTQPATH ...]] -g GENOME -r
REFERENCE FOLDER

optional arguments:
-h, --help show this help message and exit
-f [FASTQPATH [FASTQPATH ...]], --fastqs [FASTQPATH [FASTQPATH ...]]
Path(s) to fastq files, multiple paths can be provided
together. eg. &quot;-f path1 path2&quot;
-g GENOME, --genome GENOME
Genome build, e.g. &quot;hg38&quot;, &quot;mm10&quot;
-r REFERENCE FOLDER, --reference REFERENCE FOLDER
Reference folder for alignment. VDJ reference is
needed if subcommand &quot;vdj&quot; is used.
</code></pre>

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