Help Needed with readDepth Tool Installation and Usage

[indxAi]

I am reaching out to you regarding an issue I encountered while attempting to use your readDepth tool for copy number alteration analysis on your test data. Specifically, I installed the tool manually in the Ubuntu terminal.

However, I have encountered an error that I am unsure how to resolve. When executing the following line of code:

> rdo <- new("rdObject")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") : cannot open file 'params': No such file or directory

[chrisamiller]

If you closely follow the instructions in the main README, it describes a specific directory structure that needs to be set up, including a "params" file, which appears to be missing in your case.

[indxAi]

I've carefully followed the instructions in the main README, including setting up the specified directory structure and ensuring that the "params" file is in place. Despite these efforts, I'm still encountering the same error.

[chrisamiller]

Is your working directory the same one that contains the params file? getwd()

[indxAi]

yes,

> getwd()
[1] "/home/ankit.yadav/readDepth/working_directory"

(base) ankit.yadav@icare-pipeline:~/readDepth/working_directory$ la *
params

annotations:
entrypoints.hg19.male  gcWinds  mapability

output:

reads:
chr1.bed

[chrisamiller]

Strange... I don't have a clear explanation for that behavior. Off the top of my head: permissions issues? If you try it manually with something like read.table("params") can it find the file?

[indxAi]

I read the README file for annotation but didn't understand how to create mapabilty and gc content files. like which input should I use? and how can I run those 3 scripts