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Stereoseq workflow analysis

Dear all,

Hope you are well. I recently performed spatial transcriptomic using Stereoseq workflow. The Sequencing core has performed the alignment and I got all the files back like one in the attach and my samples were sequenced using Tissue Microarray (TMA).

I asked ChatGPT to find suitable R or python package to perform the full analysis. It recommended Giotto. So far, i could not make it to work yet. From your experience, what is the R/python package suitable for Steroseq analysis.

Latest version of Giotto is 4.2.2. It also provided workflow for Stereoseq https://giottosuite.com/articles/stereoseq_mouse_eyeball.html. However, with this latest version of 4.2.2, I could not get the function "createGiottoStereoSeqObject". Could anyone help me? if you happen to point me to the complete workflow in R

Thanks,

Synat,

enter image description here

spatial transcriptomic
• 502 views • link
written by Synat • Synat

1 answer

Hello.

I have bad news and good news. The good news is that I had the same issue and I think I managed to resolve it.

  1. Define the path to your specific GEF file
gef_fp <- file.path(data_path, "C04687E314.tissue.gef")
  1. Use the specialized GEF converter
g <- GiottoClass::gefToGiotto(
  gef_file = gef_fp,
  bin_size = "bin100",
  verbose = TRUE
)
  1. Quickly check if it worked
g

So I get dimensions : 26466, 1309 (features, cells).

Bad news: In the tutorial it should be "At this bin size, this dataset has 1309 bins and 26535 genes." I mean not bad. SO when I moved on to proceed my image keeps saying "Warning message: image 'HE_image' is not within the plotting window " which does not show me the image.

Hope I helped :)

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updated by GenoMax GenoMax • written by tatsispolychronis • tatsispolychronis

Thanks, you very much for taking time helping me. Would you recommend Stereopy python package?

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written by Synat • Synat

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