One file missing

[julgrandvallet]

Description:

While following the workflow provided in the repository, I'm encountering an issue where I cannot find the file GTEx_counts_Marginal_Outliers.csv which causes the subsequent Python script to fail.

Steps to Reproduce:

1. Set up the environment using the provided conda commands.
2. Set the necessary directories and paths.
3. Download data using the wget commands and gunzip them.
4. Run the R command to render the GTEx_data_preparation.Rmd.
5. Observe that GTEx_counts_Marginal_Outliers.csv file is not generated.

Environment:

Operating System: Pop!_OS 22.04 LTS (Ubuntu based)
R Version: 4.3.1 (2023-06-16) -- "Beagle Scouts"
Python Version: Python 3.9.13
Conda Version: conda 22.9.0

Additional Information:

I have verified that all wget commands ran successfully and all necessary files were downloaded. All paths and directories were set as instructed.

Temporary Solution:

To obtain the missing GTEx_counts_Marginal_Outliers.csv file, I followed these steps in R:

# Read the .RDS file
data <- readRDS("GTEx_counts_Marginal_Outliers.RDS")

# Extract the counts matrix
counts_matrix <- assay(data, "counts")

# Save the matrix as a .csv file
write.csv(counts_matrix, "GTEx_counts_Marginal_Outliers.csv", row.names = TRUE)

Ps: I'm sorry for that first Issue, uploaded it wrongly. Thank you all.