where is build_matrix_original.R？

[QuanlongJiang]

I believe it is essential to analyze from the raw sequencing data, but I can't find it.

[ksmcu]

I believe it is essential to analyze from the raw sequencing data, but I can't find it.

Hello, have you by any chance found the build_matrix_original.R file? I was trying to use scASfind but am having a hard time locating this file.

[YY-SONG0718]

Hello, I am not sure where you encounter the need to get the build_matrix_original.R? Please kindly remind me so I can update it.

The latest pipeline is the scripts/create_index.R and I have incorporated all functions in build_matrix_original.R to this file.

[ksmcu]

Hi,

Thank you for your response and for developing scASfind. I found this issue in the vignettes/example_workflow.ipynb file, specifically in Section 1.4 Build Custom Index, in block 26. The comment states: "first read in all the matrix generated from running build_matrix_original.R."

However, in the previous block (block 25), I noticed that you indicate running the create_index.R file instead. So, I am currently using the create_index.R file for my analysis.

May I ask another question? In the create_index.R file, the expected input is a combined cell pools PSI matrix, which is the output of Whippet. I wanted to confirm the format of this file. Since I ran Whippet directly on each individual cell, I have all the required columns for create_index.R, except for the Sample column. I was wondering if it would be acceptable for me to concatenate all the Whippet outputs from individual cells and manually add the Sample column myself?

I really appreciate your response.