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aerickso / SpatialInferCNV

Clone Calling from Visium Spatial Transcriptomics of Cancer samples
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Tutorial issue #13

Open patruong opened 3 weeks ago

patruong commented 3 weeks ago

I'm currently going through you tutorial https://aerickso.github.io/SpatialInferCNV/

I am having a problem with reaching this file siCNV_GeneOrderFile.tsv from your link. I created my own .gtf file to proceed with the tutorial, but am now getting stuck att obtaining the infercnv.21_denoised.observations_dendrogram.txt file needed to complete the tutorial. Can you help me with this? Specifically, this code line part

BreastCancer10x_for_clustering <- read.dendrogram(file = "./UserGuideFiles/infercnv.21_denoised.observations_dendrogram.txt")

bahnsterian commented 2 weeks ago

I am having the similar issue. I cannot locate the infercnv.21_denoised.observations_dendrogram.txt in the output folder.

Edit: @patruong : This might help. https://github.com/broadinstitute/infercnv/issues/592#issuecomment-1701827284

snowwingfly commented 2 weeks ago

I am having the same problem, too. I cannot find the infercnv.21_denoised.observations_dendrogram.txt in the output folder. Can you help me with this?