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czarnewski / ilc_tissue_imprinting

Repository contacting the code related to the article "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing" Mazzurana, Czarnewski et al (2020) Cell Research
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script_path are missing in run_workflow.sh #1

Open zhangpicb opened 1 year ago

zhangpicb commented 1 year ago

Dear @czarnewski

Thanks for your beautiful paper and code!

I want to use scRNA-seq data with cell type annotation to deconvolution my bulk RNA-seq.

But I only find scRNA-seq raw data and codes.And the _scriptpath in _runworkflow.sh is not found in this repo.

https://github.com/czarnewski/ilc_tissue_imprinting/blob/4a3f8a3c9b8a6058db4ede4cc946b05e0794b93d/run_workflow.sh#LL74C10-L74C21

Thanks in advanced!

czarnewski commented 1 year ago

Hi @zhangpicb , Thank you for the interest in our paper and code! Maybe you forgot to download the 3rd chunk on line 27:

#################################
### DOWNLOAD CODE FROM GITHUB ###
#################################
! test -d 'sauron' && {
  $(git clone https://github.com/NBISweden/sauron.git --branch v.0.1-beta)
}
script_path=$main/'sauron/scripts'

Give it a try and let me know if you face other issues. Cheers, Paulo