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danieljrichard / Code-scripts-used-for-Banerjee-et-al.-2021

Code/scripts used for RNA-seq analyses pertaining to Banerjee et al. 2021
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Running issue #1

Open ParnianH98 opened 2 years ago

ParnianH98 commented 2 years ago

Hi I am trying to run your code to extract DE genes from the dataset, and I have some issues. I am new to this package, but it seems the files function "tximport" required are not prepared in GitHub. If I want to explain more, while I run this code, I get the following error:

"Error in tximport(as.character(metadata_curate$FILE), type = "salmon", : length(files) > 0 is not TRUE"

Any suggestion on my problem would be appreciated.

danieljrichard commented 2 years ago

Hello, You'll need to load the 'library(tximport)' line in order to load the tximport library required to run this GitHub code. With regards to your immediate concert, the 'length(files) > 0 is not TRUE' issue would, I suspect, be related to the metadata_curate object not having a 'FILE' entry. Could you confirm whether there is a column in this dataframe named FILE full of .sf file paths?