SAW 参数命令

可在命令行输入saw --help | -h,查看具体分析流程和参数设置信息,通过 saw --version 检查软件版本信息。

SAW count

将时空转录组测序数据转换为空间特征表达矩阵。

运行方式: saw count [Parameters] --id <ID> --sn <SN> --omics <OMICS> --kit-version <TEXT> --sequencing-type <TEXT>--reference <PATH> --image <IMG> --fastqs <PATH>

saw count -h | --help

ParameterDescription
--id <ID>(Optional, default to None) A unique task id ([a-zA-Z0-9_-]+) which will be displayed as the output folder name and the title of HTML report. If the parameter is absent, --sn will play the same role.
--sn <SN>(Required, default to None) SN (serial number) of the Stereo-seq chip.
--omics <OMICS>(Required, default to "transcriptomics") Omics information. "transcriptomics,proteomics" for Stereo-CITE analysis.
--kit-version <TEXT>(Required, default to None) The version of the product kit. More in count pipeline introduction.
--sequencing-type <TEXT>(Required, default to None) Sequencing type of FASTQs which is recorded in the sequencing report.
--chip-mask <MASK>(Required, default to None) Stereo-seq chip mask file.
--organism <TEXT> (Optional, default to None) Organism type of sample, usually referring to species.
--tissue <TEXT> (Optional, default to None) Physiological tissue of sample.
--reference <PATH>(Optional, default to None) Path to the reference folder, containing SAW-compatible index files and GTF/GFF, built by SAW makeRef.
--ref-libraries <CSV>(Optional, default to None) Path to a ref_libraries.csv which declares reference indexes, built by SAW makeRef. Not compatible with --reference.
--fastqs <PATH>(Required, default to None) Path(s) to folder(s), containing all needed FASTQs. If FASTQs are stored in multiple directories, use it as: --fastqs=/path/to/directory1,/path/to/directory2,.... Notice that all FASTQ files under these directories will be loaded for analysis.
--adt-fastqs <PATH>(Optional, default to None) Path(s) to folder(s), containing all ADT FASTQs. If FASTQs are stored in multiple directories, use it as: --adt-fastqs=/path/to/directory1,/path/to/directory2,.... Notice that all FASTQ files under these directories will be loaded for analysis. Also, use --fastqs specifies all gene expression FASTQs.
--microorganism-detect(Optional, default to None) Whether to perform analysis related to microorganisms. Notice that the detection only works for FFPE assay currently.
--uniquely-mapped-only(Optional, default to None) Only annotate on uniquely mapped reads during read annotation.
--rRNA-remove(Optional, default to None) Whether to remove rRNA. Before turning the switch on, make sure that the necessary rRNA information has been added to FASTA, using SAW makeRef.
--clean-reads-fastq(Optional, default to None) Whether to output the Clean Reads (before RNA alignment) in FASTQ format, which have undergone CID mapping, RNA filtering, and MID filtering.
--unmapped-STAR-fastq(Optional, default to None) Whether to output unmapped reads in FASTQ format.
--unmapped-fastq(Optional, default to None) Whether to output unmapped reads in FASTQ format (not including "too many loci" reads from STAR).
--image <TIFF>(Optional, default to None) TIFF image for QC (quality control), combined with expression matrix for analysis.
Name rule for input TIFF :
a. <SN>_<stain_type>.tif
b. <SN>_<stain_type>.tiff
c. <SN>_<stain_type>.TIF
d. <SN>_<stain_type>.TIFF
<stainType> includes:
a. ssDNA
b. DAPI
c. HE (referring to H&E)
d. <IF_name1>_IF, <IF_name2>_IF, ...
--image-tar <TAR>(Optional, default to None) The compressed image .tar.gz file from StereoMap has been through prepositive QC (quality control).
--output <PATH> (Optional, default to None) Set a specific output directory for the run.
--threads-num <NUM>(Optional, default to 8) Allowed local cores to run the pipeline.
--memory <NUM>(Optional, default to detected) Allowed local memory to run the pipeline.
--gpu-id <NUM>(Optional, default to -1) Set GPU id, according to GPU resources in the computing environment. Default to -1, which means running the pipeline using the CPU.
-h, --help(Optional, default to None) Print help information.

SAW makeRef

构建参考基因组的索引文件,支持 SAW count 分析,需输入 GTF/GFF 注释文件和 FASTA 基因组文件,可以加入 rRNA 信息的 FASTA 文件。

运行方式: saw makeRef [Parameters] --mode <MODE> --fasta <FASTA> --gtf <GTF/GFF> --genome <PATH>

saw makeRef -h | --help

ParameterDescription
--mode <MODE>(Required, default to "STAR") Set the mode to build index files, used for the alignment. There are three modes, including STAR, Bowtie2 and Kraken2 for specific analysis scenarios.
--fasta <FASTA>(Optional, default to None) Path to FASTA, to build index files. When it comes to multiple FASTAs, they will be integrated in order of input beforehand.
--rRNA-fasta <FASTA>(Optional, default to None) Path to rRNA FASTA that will be added to --fasta file, with the elimination of redundant rRNA fragments.
--gtf <GTF/GFF>(Optional, default to None) Path to input GTF/GFF to build index files.
--basename <TEXT>(Optional, default to "host") Basename for Bowtie2 index files when set mode=Bowtie2. If not specified, "host" will be used, which straightforwardly means removing host information in the next step.
--database <DATABASE>(Optional, default to None) Path to Kraken2 reference database. If the parameter works, output index files will be saved in the same directory level.
--genome <PATH>(Optional, default to detected) Path to the output reference genome with index information.
--params-csv <CSV>(Optional, default to detected) Path to CSV file, recording detailed parameters to build Bowtie2/Kraken2 index. It works when --mode is set to Bowtie2/Kraken2. More in the makeRef tutorial.
--threads-num <INT>(Optional, default to 8) Set the number of threads to use.
-h, --help(Optional, default to None) Print help information.

SAW checkGTF

检查 GTF/GFF 注释文件是否为标准格式。此外,可以从 GTF/GFF 中提取特定的注释信息。

运行方式: saw checkGTF [Parameters] --input-gtf <GTF/GFF> --attribute <key:value> --output-gtf <GTF/GFF>

saw checkGTF -h | --help

ParameterDescription
--input-gtf <GTF/GFF>(Required, default to None) Path to input GTF/GFF, for a necessary format check.
--attribute <key:value>(Optional, default to None) Extract specific annotation information from GTF/GFF. Input as <gene_biotype:protein_coding>.
--output-gtf <GTF/GFF>(Required, default to None) Path to output GTF/GFF after a necessary check, or additional filtration when performing --attribute.
-h, --help(Optional, default to None) Print help information.

SAW realign

接回 StereoMap 手动处理后生成的图像文件,重启分析流程。

运行方式: saw realign [Parameters] --id <ID> --sn <SN> --count-data <PATH> --realigned-image-tar <TAR>

saw realign -h | --help

ParameterDescription
-id <ID>(Optional, default to None) A unique task id ([a-zA-Z0-9_-]+) which will be displayed as the output folder name and the title of HTML report. If the parameter is absent, --sn will play the same role.
--sn <SN>(Required, default to None) SN (serial number) of the Stereo-seq chip.
--count-data <PATH>(Required, default to None) Output folder of the corresponding SAW count result, which mainly contains the expression matrices and other related datasets.
--realigned-image-tar <TAR>(Required, default to None) Compressed image file from StereoMap, which has been manually processed, including stitching, tissue segmentation, cell segmentation, calibration and registration.
--lasso-geojson <GEOJSON>(Optional, default to None) Lasso GeoJSON from StereoMap is used for tissue segmentation when the analysis is without images. It is incompatible with --realigned-image-tar.
--adjusted-distance <INT>(Optional, default to 10) Outspread distance based on the cellular contour of the cell segmentation image, in pixels. Default to 10. If --adjusted-distance=0, the pipeline will not expand the cell border.
--no-matrix(Optional, default to None) Whether to output feature expression matrices.
--no-report(Optional, default to None) Whether to output HTML report.
--output <PATH>(Optional, default to None) Set a specific output directory for the run.
--threads-num <NUM>(Optional, default to 8) Set the number of threads to use.
--gpu-id <NUM>(Optional, default to -1) Set GPU id, according to GPU resources in the computing environment. Default to -1, which means running the pipeline using the CPU.
-h, --help(Optional, default to None) Print help information.

SAW reanalyze

进行数据再分析,包含聚类分析、矩阵套索和差异表达分析。

运行方式: saw reanalyze [Parameters] --gef <GEF> --bin-size <INT> --marker --output <PATH>

saw reanalyze -h | --help

cluster

ParameterDescription
--gef <GEF>(Optional, default to None) Input bin GEF file for analysis.
--cellbin-gef <GEF>(Optional, default to None) Input cellbin GEF file for analysis.
--bin-size <INT or LIST>(Optional, default to 200) Bin size for analysis.
--Leiden-resolution <FLOAT>(Optional, default to 1.0) The resolution parameter controls the coarseness of the clustering when performing Leiden. Higher values lead to more clusters.
--marker(Optional, default to None) Whether to perform differential expression analysis.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.
--threads-num <NUM>(Optional, default to 8) Set the number of threads to use.

lasso

ParameterDescription
--gef <GEF>(Optional, default to None) Input bin GEF file for analysis.
--cellbin-gef <GEF>(Optional, default to None) Input cellbin GEF file for analysis.
--bin-size <INT or LIST>(Optional, default to 200) Bin size for analysis.
--lasso-geojson <GEOJSON>(Optional, default to None) GeoJSON from StereoMap to lasso sub expression matrices of targeted regions.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.

diffExp

ParameterDescription
--count-data <PATH>(Optional, default to None) Output folder of the corresponding SAW count result, which mainly contains the expression matrices and other related datasets.
--diffexp-geojson <GEOJSON>(Optional, default to None) GeoJSON from StereoMap to analyze differential expression.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.

multiomics

ParameterDescription
--gef <GEF LIST>(Optional, default to None) Input protein and gene bin GEF files for analysis, separated by comma.
--cellbin-gef <GEF LIST>(Optional, default to None) Input protein and gene cellbin GEF files for analysis, separated by comma.
--bin-size <INT>(Optional, default to 200) Bin size for analysis.Recommended to use 20 and 50.
--protein-panel <PANEL>(Optional, default to None) Path to a ProteinPanel.list. Not compatible with --ref-libraries.
--ref-libraries <CSV>(Optional, default to None) Path to a ref_libraries.csv which declares protein panel. Not compatible with--protein-panel.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.
--gpu-id <NUM>(Optional, default to -1) Set GPU id, according to GPU resources in the computing environment. Default to -1, which means running the pipeline using the CPU.
--threads-num <NUM>(Optional, default to 8) Set the number of threads to use.

midFilter

ParameterDescription
--gef <GEF>(Required, default to None) Input bin GEF file for analysis.
--mid-json <JSON>(Required, default to None) JSON from StereoMap to manually filter spatial expression matrixces by MID range.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.

removeBackground

ParameterDescription
--gef <GEF>(Required, default to None) Input bin protein GEF file for analysis
--bin-size <INT>(Required, default to None) Bin size for analysis. Recommended to use 20 and 50.
--protein-panel <PANEL>(Optional, default to None) Path to a ProteinPanel.list. Not compatible with --ref-libraries.
--ref-libraries <CSV>(Optional, default to None) Path to a ref_libraries.csv which declares protein panel. Not compatible with--protein-panel.
--output <PATH>(Optional, default to None) Path to the output folder, to save analysis results.

SAW convert

实现数据格式转换,分析流程下设置子模块用于实现特定的转换需求。

运行方式: saw convert gef2gem [Parameters] --gef <GEF> --bin-size <INT> --marker --gem <GEM>

saw convert -h | --help

ParameterDescription
--threads-num <NUM>(Optional, default to 8) Set the number of threads to use.
-h, --help(Optional, default to None) Print help information.

gef2gem

ParameterDescription
--gef <GEF>(Required, default to None) Path to input bin GEF file.
--bin-size <INT>(Optional, default to 1) Bin size used during conversion.
--cellbin-gef <GEF>(Optional, default to None) Path to input cellbin GEF file.
--gem <GEM>(Optional, default to None) Path to output GEM file.
--cellbin-gem <GEM>(Optional, default to None) Path to output cellbin GEM file.

gem2gef

ParameterDescription
--gem <GEM>(Optional, default to None) Path to input GEM file.
--gef <GEF>(Optional, default to None) Path to output bin GEF file.
--cellbin-gem <GEM>(Optional, default to None) Path to output cellbin GEM file.
--cellbin-gef <GEF>(Optional, default to None) Path to input cellbin GEF file.

bin2cell

ParameterDescription
--gef <GEF>(Required, default to None) Path to input bin GEF file.
--image <TIFF>(Required, default to None) Path to the image of cell segmentation.
--cellbin-gef <GEF>(Required, default to None) Path to output cellbin GEF file.
--cellbin-gem <GEM>(Optional, default to None) Path to output cellbin GEM file.

gef2h5ad

ParameterDescription
--gef <GEF>(Optional, default to None) Path to input bin GEF file.
--bin-size <INT>(Optional, default to 20) Bin size used during conversion.
--cellbin-gef <GEF>(Optional, default to None) Path to input cellbin GEF file.
--h5ad <H5AD>(Required, default to None) Path to output AnnData H5AD file.

gem2h5ad

ParameterDescription
--gem <GEM>(Optional, default to None) Path to input GEM file.
--bin-size <INT>(Optional, default to 20) Bin size used during conversion.
--cellbin-gem <GEM>(Optional, default to None) Path to input cellbin GEM file.
--h5ad <H5AD>(Required, default to None) Path to output AnnData H5AD file.

gef2img

ParameterDescription
--gef <GEF>(Required, default to None) Path to input bin GEF.
--bin-size <INT>(Required, default to 1) Bin size used to plot expression heatmap.
--image <TIFF>(Required, default to None) Path to output heatmap image.

visualization

ParameterDescription
--gef <GEF>(Required, default to None) Path to input raw bin GEF file.
--bin-size <INT>(Required, default to 1,5,10,20,50,100,150,200) Bin sizes used during conversion.
--visualization-gef <GEF>(Required, default to None) Path to output visualization GEF file.

tar2img

ParameterDescription
--image-tar <TAR>(Required, default to None) Path to input image compressed tar file.
--image <PATH>(Required, default to None) Path to output folder of images.

img2rpi

ParameterDescription
--image <TIFF>(Required, default to None) Path to images, please note that the order of input images, corresponding to --layers names.
--layers <TEXT>(Required, default to None) Layer names, recorded in the output RPI file, should correspond to images individually. Layer names can be set arbitrarily, but follow the format of <stain_type>/<image_type>, like DAPI/TissueMask.
--rpi <RPI>(Required, default to None) Path to output RPI file.

merge

ParameterDescription
--image <TIFF>(Required, default to None) Path to input images (up to 3), to be merged into one image, in the color order of R-G-B.
--merged-image <TIFF>(Required, default to None) Path to output multichannel image.

overlay

ParameterDescription
--image <TIFF>(Required, default to None) Path to image, used to be the base one.
--template <TXT>(Required, default to None) Point information of matrix template.
--overlaid-image <TIFF>(Required, default to None) Path to output overlaid image, with the cover of a template.
© 2025 STOmics Tech. All rights reserved.Modified: 2025-03-07 10:28:04

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