Phred Parameter File Problems

转载来源：http://www.codoncode.com/support/faqs/phedpar.html#Explanation

关联：http://blog.sina.com.cn/s/blog_6a6c136d0100xc3f.html

1. vim phredpar.dat     ##打开phredpar.dat  

Operating system	Default location	File name
Windows (98, ME, NT4, 2000, XP)	C:\Program files\CodonCode\	phredpar.dat
Linux & UNIX	/usr/local/genome/lib/	phredpar.dat
OS X	/usr/local/genome/lib/	phredpar.dat
Classic Mac OS	"Preferences" folder in the "System Folder" on your startup disk	PhredParameters

Operating system	Suggested editor
Windows (98, ME, NT4, 2000, XP)	NotePad
Linux & UNIX	gedit, emacs, vi, or similar
OS X	TextEdit or BBEdit
Classic Mac OS	SimpleText

2.

 "DT3700POP5{BDv3}.mob"    <chemistry>    <dye type>   <machine type> # 根据warnings添加

You should know the chemistry, dye type, and machine; if in doubt, as the people who did the sequencing. 

The name here indicates terminator ("DT"), big dye (BD) chemistry from ABI3700. 

In the Phred parameter file, we find a very similar line:

"DT3700POP5{BDv3}v1.mob"	terminator	big-dye	                ABI_3700

After copy, paste, and editing, we now have two lines like this:

"DT3700POP5{BDv3}v1.mob"	terminator	big-dye	                ABI_3700
"DT3700POP5{BDv3}.mob"		terminator	big-dye	                ABI_3700

3. ESC --- :wq   ##save the file

##Find a line that is close to what you want; 

##copy and paste it; and then edit the line so that it exactly shows the "primer ID string" in the Phred error message. 

##Then save the file .