Run SeekSoulTools

Run tests

Example 1: T cell receptor analysis example

seeksoultools vdj run \
--fq1 /path/to/demo_tcr/demo_tcr_R1.fq.gz \
--fq2 /path/to/demo_tcr/demo_tcr_R2.fq.gz \
--chemistry DD5V1 \
--samplename demo_tcr \
--chain TR \
--core 16  \
--outdir /path/to/ouput/demo_tcr \
--organism human

Example 2: B cell receptor analysis example

seeksoultools vdj run \
--fq1 /path/to/demo_bcr/demo_bcr_R1.fq.gz \
--fq2 /path/to/demo_bcr/demo_bcr_R2.fq.gz \
--chemistry DD5V1 \
--samplename demo_bcr \
--chain IG \
--core 16  \
--outdir /path/to/ouput/demo_bcr \
--organism human

Parameter descriptions

Parameters	Descriptions
–fq1	Paths to R1 fastq files.
–fq2	Paths to R2 fastq files.
–samplename	Sample name. Only digits, letters, and underscores are supported
–chemistry	Reagent type, with each type corresponding to a combination of --shift, --pattern, --structure, --barcode, and --sc5p. Available options: DD5V1. DD-Q corresponds to the SeekOne® DD Single Cell Immune Profiling Kit.
–organism	organism, Available options: human，mouse， monkey，rabbit or rat.
–chain	chain type, Available options: IG and TR. IG for B clel receptor and TR for T cell receptor.
–core	Number of threads used for the analysis
–outdir	Output directory. Absolute path, and ensure that the outdir for each task is unique.
–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.