Run SeekArcTools

Run tests

Example 1: Basic usage

Set up the necessary configuration files for the analysis, including sample data paths, reference genome paths, etc. Run the SeekArcTools using the following command:

seekarctools_py arc run \
    --rnafq1 /path/to/demo/demo_GE_S1_L001_R1_001.fastq.gz \
    --rnafq2 /path/to/demo/demo_GE_S1_L001_R2_001.fastq.gz \
    --atacfq1 /path/to/demo/demo_arc_S2_L002_R1_001.fastq.gz \
    --atacfq2 /path/to/demo/demo_arc_S2_L002_R2_001.fastq.gz \
    --samplename demo \
    --outdir /path/to/outdir \
    --refpath /path/to/reference/GRCh38 \
    --include-introns \
    --core 16

Example 2: Adjusting thresholds for re-running peak calling or cell calling

If the identified peaks or cells under default parameters do not meet requirements, users can adjust parameters to skip preceding steps (e.g., alignment) and re-run the workflow to optimize results while saving time.

seekarctools_py arc retry \
    --samplename demo \
    --outdir /path/to/outdir \
    --refpath /path/to/reference/GRCh38 \
    --core 16 \
    --qvalue 0.01 \
    --snapshift 0 \
    --extsize 200 \
    --min_len 200 \
    --min_atac_count 1000 \
    --min_gex_count 500

• Note: Ensure all files from previous runs remain intact and are not deleted or relocated. The --outdir specifies the directory path from the initial seekarctools analysis. The --min_atac_count must be used together with --min_gex_count; it will not take effect if used alone.

Parameter descriptions

Parameters	Parameter descriptions
–rnafq1	Paths to R1 fastq files of RNA library
–rnafq2	Paths to R2 fastq files of RNA library
–atacfq1	Paths to R1 fastq files of ATAC library
–atacfq2	Paths to R2 fastq files of ATAC library
–samplename	Sample name
–outdir	output directory. Default: ./
–skip_misB	If enabled, no base mismatch is allowed for barcode. Default is 1.
–skip_misL	If enabled, no base mismatch is allowed for linker. Default is 1.
–skip_multi	If enabled, discard reads that can be corrected to multiple white-listed barcodes. Barcodes are corrected to the barcode with the highest frequency by default.
–skip_len	Skip filtering short reads after adapter filter, short reads will be used.
–core	Number of threads used for the analysis.
–include-introns	When disabled, only exon reads are used for quantification. When enabled, intron reads are also used for quantification.
–refpath	The path of reference genome.
–star_path	External STAR software path. If the index in the reference genome is built by another STAR, please specify its path.
–qvalue	Minimum FDR (q-value) cutoff for peak detection. Default: 0.05.
–nolambda	If True, MACS3 will use the background lambda as local lambda. This means MACS3 will not consider the local bias at peak candidate regions.
–snapshift	MACS3 peak detection shift size. Default: 0.
–extsize	MACS3 peak detection extension size. Default: 400.
–min_len	Minimum length of peaks. If not set, it will be set to “extsize”. Default: 400.
–broad	If enabled, perform broad peak calling and generate results in UCSC gappedPeak format, which encapsulates the nested structure of peaks.
–broad_cutoff	Threshold for broad peak calling. Default: 0.1.
–min_atac_count	Cell caller override: define the minimum number of ATAC transposition events in peaks (ATAC counts) for a cell barcode.
–min_gex_count	Cell caller override: define the minimum number of GEX UMI counts for a cell barcode.
-h，–help	Show this parameter descriptions.