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jfnavarro / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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Having trouble understanding how to use this pipeline with Real world Spatial Data. #102

Open adiv5 opened 1 year ago

adiv5 commented 1 year ago

Hi, I am trying this out on the example visium10x dataset for prostate cancer (https://www.10xgenomics.com/resources/datasets/human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0)

My end usecase is to have a basic Image Model that could predict gene expression for a given gene on the entire tissue on cell level

in this data, in the input files section, we have Fastq files and a probeset file thats it. For the other output files im not sure if those could be used / need to be used in here.

If you could help with some concrete steps to use this , it would really help a lot.

Thank you in advance.

jfnavarro commented 1 year ago

Hi @adiv5

I'm not entirely sure I understand your question. You can use the st_pipeline to process the raw data (FASTQ) to obtain a matrix of counts (spots by genes). This matrix can be used, together with the HE image, for downstream analyses such as the one you mention but the st_pipeline will not do that for you.

Best, Jose