Run Seeksoultools
Run tests
Example 1: Basic usage
mkdir -p /demo/myproject/
cd /demo/myproject/
seeksoultools rna run \
--fq1 /demo/data/demo3k_R1_001.fastq.gz \
--fq2 /demo/data/demo3k_R2_001.fastq.gz \
--samplename demo3k \
--outdir /demo/myproject/ \
--genomeDir /demo/refdata/GRCh38-3.0.0/star \
--gtf /path/demo/refdata/GRCh38-3.0.0/genes/genes.gtf \
--chemistry MM \
--core 4
Example 2: Specify a different version of STAR for analysis. Make sure that the STAR version is compatible with the –genomeDir.
mkdir /demo/myproject/
cd /demo/myproject/
seeksoultools rna run \
--fq1 /demo/data/demo3k_R1_001.fastq.gz \
--fq2 /demo/data/demo3k_R2_001.fastq.gz \
--samplename demo3k \
--outdir /demo/myproject/ \
--genomeDir /demo/refdata/GRCh38/star \
--gtf /path/demo/refdata/GRCh38/genes/genes.gtf \
--chemistry MM \
--core 4 \
--star_path /path/to/cellranger-5.0.0/lib/bin/STAR
Example 3: A sample has multiple sets of fastq files
mkdir /demo/myproject/
cd /demo/myproject/
seeksoultools rna run \
--fq1 /demo/data/demo_S1_L001_R1_001.fastq.gz \
--fq1 /demo/data/demo_S1_L002_R1_001.fastq.gz \
--fq2 /demo/data/demo_S1_L001_R2_001.fastq.gz \
--fq2 /demo/data/demo_S1_L002_R2_001.fastq.gz \
--samplename demo \
--outdir /demo/myproject/ \
--genomeDir /demo/refdata/GRCh38/star \
--gtf /demo/refdata/GRCh38/genes/genes.gtf \
--chemistry MM \
--core 4
Example 4: Customize the structure of R1
seeksoultools rna run \
--fq1 /demo/data/demo3k_R1_001.fastq.gz \
--fq2 /demo/data/demo3k_R2_001.fastq.gz \
--samplename demo \
--outdir /demo/myproject/ \
--genomeDir /demo/refdata/GRCh38/star \
--gtf /demo/refdata/GRCh38/genes/genes.gtf \
--barcode /demo/utils/CLS1.txt \
--barcode /demo/utils/CLS2.txt \
--barcode /demo/utils/CLS3.txt \
--linker /demo/utils/Linker1.txt \
--linker /demo/utils/Linker2.txt \
--structure B9L12B9L13B9U8 \
--core 4
The structure of read1 is represented by
B9L12B9L13B9U8
, which means it consists of three sections of cell barcode, each with 9 bases, and a UMI section with 8 bases. The linker section between the cell barcode and UMI consists of two parts, with the first part being 12 bases and the second part being 13 basesUse
--barcode
to specify the three sections of barcodes sequentially, and use--linker
to specify the two sections of linkers sequentially.
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. |
–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 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 |