Run SeekSoulTools
Run tests
Example 1: Basic usage
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 \
--rRNAgenomeDir /path/to/hg38_rRNA/star \
--rRNAgtf /path/to/hg38_rRNA/genes/delete_rRNA5.8-18-28_in_rRNA45s.gtf \
--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 |
–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 |