Tutorial:Downloading GnuWin and using to convert txt to bed file for windows users
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8 months ago

I had alot 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 incase 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 its 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 txt bed2txt sequencing Tutorial • 392 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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