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Pipelines

Pipelines in SAW generally assemble several programming modules which are designed to handle specific analysis tasks individually, for diverse requirements.

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Main pipeline

SAW count is the central component of the software suite, compatible with most Stereo-seq FF and Stereo-seq FFPE datasets. The inputs consist of a chip mask, FASTQ files, a reference and a microscope image. So that the pipeline counts gene expression reads to generate expression matrices and analysis results from the Stereo-seq chip.

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Complementary pipelines

The complementary pipelines include:

  • SAW makeRef: prepare for the reference index files. GTF/GFF and FASTA files or additional specific rRNA FASTA files are needed;

  • SAW chechGTF: check whether an annotation file (GTF/GFF) is in the standard format, used in SAW count. In addition, extract specific information from GTF/GFF;

  • SAW realign: accept the modified image .tar.gz from StereoMap, to generate the results of manual processes;

  • SAW reanalyze: reanalyze the matrices to generate results, including clustering analysis, lasso and differential expression analysis;

  • SAW convert: provide tools for file format conversions;

of which the purpose is to support the main pipeline SAW count and ensure smooth, convenient processing of the entire analysis.

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