batchRenaming_script/linux/README.md

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Batch file renaming (for Linux)

IMPORTANT! These two files (1_get_filenames.bat + 2_rename_files.bat) must be within the folder with all FCS files to be processed... or run them from folder with FCS files.

1. Run 1_get_filenames.sh. This file performs two operations:

   • Replaces all spaces in filenames with underscores.
   • Creates a text file called list_filenames.txt with all FCS files whithin this folder.

2. Open the text file in Excel (or whatever text editor you want) and, in the next column to that one with filenames, write the new name for each FCS file. Do not create a header in Excel. Save it as txt (without change its name)!!

       filename1   newname1
       filename2   newname2
               ...
               ...
   

3. Run 2_rename_files.sh and automatically all files will be renamed to new names.

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.