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STOmics / SAW

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How to process data without mask files #141

Open youwh1996 opened 4 weeks ago

youwh1996 commented 4 weeks ago

I downloaded stereo-seq data from public database. However, they did not provide the mask h5 files. How I can run the SAW pipeline

Clouate commented 4 weeks ago

@youwh1996 Hi, could you tell us which database did you download the stereo-seq data from? SAW could not run without the mask h5 files.

youwh1996 commented 4 weeks ago

Thank you very much for your reply. I downloaded the stereo-seq fastaq files from GSA database with accession number: HRA005647

Clouate commented 4 weeks ago

Hi, we're sorry that we are not involved in managing this database, perhaps you could contact the submitter. Because the chip barcode spatial coordinates are recorded in the h5 file, it is necessary for Stereo-seq analysis.