Run SeekSoulTools

Run tests

Example 1: single cell full length RNA sequence data

Set up the necessary configuration files for the analysis, including the paths to the sample data, the chemistry versions, the genome index, the gene annotation file, etc. Run the SeekSoulTools using the following command:

seeksoultools fast run \
--fq1 /path/to/cellline/cellline_R1.fq.gz \
--fq2 /path/to/cellline/cellline_R2.fq.gz \
--samplename demo \
--genomeDir /path/to/GRCh38/star \
--gtf /path/to/GRCh38/genes/genes.gtf \
--chemistry DD-Q \
--include-introns \
--core 4

Example 2: Single-cell transcriptomic data from FFPE samples, using parameters --scoremin 0.2 --matchnmin 0.33

seeksoultools fast run \
--fq1 /path/to/ffpe/ffpe_R1.fq.gz \
--fq2 /path/to/ffpe/ffpe_R2.fq.gz \
--samplename demo \
--genomeDir /path/to/GRCh38/star \
--gtf /path/to/GRCh38/genes/genes.gtf \
--scoremin 0.2 \
--matchnmin 0.33 \
--chemistry DD-Q \
--include-introns \
--core 4

Parameter descriptions

Parameters	Descriptions
–fq1	Paths to R1 fastq files.
–fq2	Paths to R2 fastq files.
–samplename	Sample name. A directory will be created named after the sample name in the outdir directory. Only digits, letters, and underscores are supported.
–outdir	Output directory. Default: ./
–genomeDir	The path of the reference genome generated by STAR. The version needs to be consistent with the STAR used by SeekSoulTools.
–gtf	Path to the GTF file for the corresponding species.
–rRNAgenomeDir	The path to the reference genome generated by STAR, which is used for evaluating rRNA portion. The version needs to be consistent with the STAR used by SeekSoulTools.
–rRNAgtf	Path to the GTF file for the corresponding species, which is used for evaluating rRNA portion.
–core	Number of threads used for the analysis
–chemistry	Reagent type, with each type corresponding to a combination of --shift, --pattern, --structure, --barcode, and --sc5p. Available options: DD-Q. DD-Q corresponds to the SeekOne® DD Single Cell Full-length RNA Sequence Transcriptome-seq Kit.
–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.
–expectNum	Estimated number of captured cells.
–forceCell	When the number of cells obtained from analysis is abnormal, add this parameter with expected value N. SeekSoulTools will select the top N cells based on UMI from high to low.
–include-introns	When disabled, only exon reads are used for quantification. When enabled, intron reads are also used for quantification.
–star_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.
–scoremin	Set --outFilterScoreMinOverLread parameter of STAR. By adjusting the value, you can modify the alignment criteria for mapping reads to the reference genome for FFPE sample.
–matchnmin	Set --outFilterMatchNminOverLread parameter of STAR. By adjusting the value, you can modify the alignment criteria for mapping reads to the reference genome for FFPE sample.