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Spatial transcriptomics data

I'm working with spatial transcriptomics data. I know 10x genomics have in their web processed data and the . h5 files but the data I need it is in GEO. This public data doesn't has the. h5 file, so I have to build it, but the data doesn't has the scalefactor. json file to build the spatial object.

I checked another GEOs with spatial data and it looks like any of them have the scalefactor. json. Is there any way to contruct the object correctly with out this file? I thought this file it was necessary

Thanks in advance!

scalefactor spatial
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written by lsudupe • lsudupe

Reproducing spatial transcriptomic experiments from the GEO has been in my experience nightmarish if they don't include the proper files as part of their data upload.

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written by benformatics benformatics

yeah, I do agree with that

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written by lsudupe • lsudupe

Contact the authors and implore them to upload the necessary files (they can amend the submission). Sometimes people will submit something just to check off a requirement, without ensuring that it's actually useful; this must be avoided.

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written by seidel seidel

I already did, anyway thank you for the advice!

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written by lsudupe • lsudupe

sudupelaura : Can you post the SRA accession? Some times the original data is available under "Data Access" tab.

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written by GenoMax GenoMax

Look at their data they have the 10x BAM files and the counts, metadata, and slide image. You should be able to make some sense of the data? What are you trying to do exactly? The bams should have the aligned reads with barcodes?

,orig.ident,nCount_Spatial,nFeature_Spatial,nCount_SCT,nFeature_SCT,CM4,CM1,EndoEC,CM3,FB,EPI,Macrophage,Pericyte/SMC,EC,CM2,CM5,imagerow,imagecol
AAACGAGACGGTTGAT-1,SeuratProject,65294,8213,55779,8193,0.132981933,0.042524795,0.24858345,0.003077098,0.572832724,0,0,0,0,0,0,221.5173887,334.1885654
AAACTGCTGGCTCCAA-1,SeuratProject,64194,7513,55024,7493,0.020107703,0.399680368,0.024283936,0.006116796,0.006443315,0,0,0,0.266188388,0.011065142,0.26611435,259.7670338,280.0724009
AAAGGGATGTAGCAAG-1,SeuratProject,72093,7413,54275,7369,0.000333544,0.329455568,0,0.001797781,0,0,0.637835072,0,0.030410379,0,0.000167657,274.1224561,394.8685578
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written by benformatics benformatics

Hi! Yeah, I use this data and I am able to do the clustering and some analysis. The problem is that with out the scalefactor. json I am not able to align the spots with their position in the tissue image.

I am not sure if the. bam have the information of the alignment between the tissue and the spots

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written by lsudupe • lsudupe

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