Run

Author: SeekGene

Time: 3 min

Words: 517 words

Updated: 2026-02-26

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SeekArc™ Tools

Run Examples

Example 1: Basic Usage

Set up the necessary configuration files for analysis, including the path to sample data, reference genome path, etc. Run SeekArc™ Tools v1.1.0 using the following command:

seekarctools 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 \
    --chemistry DD_AG \
    --include-introns \
    --core 16

Example 2: Rerunning call peaks or call cell with thresholds

If the peaks or cells determined under default parameters do not meet requirements, you can adjust parameters to skip steps like alignment and rerun to save time.

seekarctools 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 that files from the previous run have not been deleted or moved. --outdir is the directory path after the first analysis with SeekArc™ Tools v1.1.0. --min_atac_count must be used together with --min_gex_count, otherwise it will not take effect.

Parameter Description

Parameter	Description
--rnafq1	Path to expression library R1 FASTQ data.
--rnafq2	Path to expression library R2 FASTQ data.
--atacfq1	Path to ATAC library R1 FASTQ data.
--atacfq2	Path to ATAC library R2 FASTQ data.
--samplename	Sample name.
--chemistry	Chemistry type. Options: DD_AG, DD5_AG.
--outdir	Output directory. Default: ./
--skip_misB	Do not allow base mismatches in barcode. Default allows one base mismatch.
--skip_misL	Do not allow base mismatches in linker. Default allows one base mismatch.
--skip_multi	Discard Reads that can be corrected to multiple whitelist barcodes. Default corrects to the barcode with the highest proportion.
--skip_len	Skip filtering short reads after adapter filtering, use short reads.
--core	Number of threads used for analysis.
--include-introns	When disabled, only exon Reads are used for quantification; when enabled, intron Reads are also used for quantification.
--refpath	Path to reference genome.
--star_path	External STAR software path. If the index in the reference genome was built by another STAR, please specify this path.
--qvalue	Minimum FDR (q-value) cutoff for peak detection. Default: 0.001.
--nolambda	If enabled, MACS3 will use background lambda as local lambda. This means macs3 will not consider local bias of peak candidate regions.
--snapshift	Shift size for MACS3 peak detection. Default: 0.
--extsize	Extension size for MACS3 peak detection. Default: 400.
--min_len	Minimum length of peak. If none, set to "extsize". Default: 400.
--broad	If enabled, perform broad peak calling, generating 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	Define the minimum number of ATAC transposition events (ATAC counts) in cell barcodes.
--min_gex_count	Define the minimum number of UMIs (GEX counts) in cell barcodes.
-h，--help	Show parameter description