multivdj

This module is used for joint analysis of 5’ RNA and VDJ data.

Run SeekSoulTools

seeksoultools multivdj run \
        --rnafq1 /path/to/demo/rna.demo.R1.fq.gz \
        --rnafq2 /path/to/demo/rna.demo.R2.fq.gz \
        --tcrfq1 /path/to/demo/tcr.demo.R1.fq.gz \
        --tcrfq2 /path/to/demo/tcr.demo.R2.fq.gz \
        --samplename demo_multi \
        --organism human \
        --core 8  \
	--genomeDir /path/to/GRCh38/star  \
        --gtf /path/to/GRCh38/genes/genes.gtf \
        --include-introns \
        --outdir ./ 

Parameter descriptions

Parameters	Descriptions
–rnafq1	The input FASTQ R1 file for RNA sequencing data. Required.
–rnafq2	The input FASTQ R2 file for RNA sequencing data. Required.
–tcrfq1	The input FASTQ R1 file for TCR sequencing data.
–tcrfq2	The input FASTQ R2 file for TCR sequencing data.
–bcrfq1	The input FASTQ R1 file for BCR sequencing data.
–bcrfq2	The input FASTQ R2 file for BCR sequencing data. Optional. Note: At least one set of parameters (–tcrfq or –bcrfq) must be specified. This can be either tcrfq1 and tcrfq2, or bcrfq1 and bcrfq2, or all four parameters.
–samplename	Sample name. A directory will be created named after the sample name in the outdir directory. Only digits, letters, and underscores are supported.
–organism	organism, Available options: human，mouse
–cfg	When the species is not human or mouse, the ref file needs to be configured by itself, and the file that records three REFs is the value of the parameter.
–core	Number of threads used for the analysis
–genomeDir	Path to another version of STAR for alignment. The version must be compatible with the –genomeDir version. The default –star_path is the STAR in the environment.
–gtf	Path to the GTF file for the corresponding species.
–include-introns	When disabled, only exon reads are used for quantification. When enabled, intron reads are also used for quantification.
–start_path	Path to another version of STAR for alignment. The version must be compatible with the –genomeDir version. The default –star_path is the STAR in the environment.