Tutorial:Downloading GnuWin and using to convert txt to bed file for windows users
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3.9 years ago

I had a lot of struggle as a beginner coding and it sucks that windows doesn't have simple built in tools like cut so I thought I'd post this in case anyone has the same problem.

This is tutorial on how to convert txt to bed files on the windows command prompt for bioinformatic novices.

Download GnuWin32 http://gnuwin32.sourceforge.net/downlinks/coreutils.php

Make sure msvcrt.dll is in your system folder (Windows\System). If it's not you can download it from https://www.dll-files.com/msvcrt.dll.html

Move GnuWin32 to C: drive

Add GnuWin32 to PATH

Control Panel>System>Advanced System settings> Environment variables>system variables

Find Path, edit one that looks like: %SYSTEMROOT%\System32\WindowsPowerShell\v1.0\ and add ;c:\GnuWin32

Run cmd under administrator

C:\GnuWin32\bin>cut -f 2,3,4,5 XXX.txt >XXX.bed

Numbers indicate columns with relevant bed file data ie. chr, start and end site, sense, id

Make sure txt file is in location cmd can find (I put in C:\GnuWin32\bin)

bed bed2txt sequencing txt • 1.4k views
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If you have Windows 10 then using WSL (Windows Subsystem for Linux is the easiest way to use unix on your Windows machine. You can then install a linux distro of your choice. Ubuntu is available in Windows app store, is popular and widely used by new users.


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