About MAQ

[James Wei]

Hi every~
I'm a beginner to use Linux and MAQ.i use this instuction to download the MAQ: svn co https://maq.svn.sourceforge.net/svnroot/maq maq.And i find the folder:maq-0.7.1,run the instruction: make -f Makefile.generic....
i already have the data of reference and read,but don't know how to use instruction:"maq fasta2bfa ref.fasta ref.bfa"?At the folder "maq-0.7.1" to run?
i always get "command not found"
I also don't find the instruction "sol2sanger"....
Please tell me the steps to run the MAQ....
Thanks a lots!!

Best,

James

[Xi Wang]

how about you typing "maq" in the command line? most probable reason is that you didn't add the dir to the environment variable "PATH".

[ffinkernagel]

if you want to run maq while you're in the folder maq-0.7.1 you'll need to type ./maq
(the ./ means the current folder. It's not in the search path for executables so you don't accidentally execute a file you were not even aware of).

[byb121]

Maq requires different formats of data as input.
You'll need to convert your reference genome and files containing reads into bfa and bfq files respectively, and then use maq to map reads to the genome.
If you installed maq correctly, command "maq" should run under any directory, at least it works this way in Ubuntu.

[James Wei]

Thank you guys~i already know how to run MAQ,i need add "./" before command ''maq''.Thank you ffinkernagel~I'm studying what can i do when i get the output file know!!!!