maq2sam command not working

[vaibhav_jain]

Hi all,
I have done alignment using Maq and have generated .map files, now I want used the aligned read to generate peaks using MACS.
For doing this I thought of converting .map file to .sam files using maq2sam command, but it showing error as unrecognized command. I have samtools installed in my system and have used samtools previously also but for maq2sam its not working, what wrong am I doing ???

Is there any other method to convert .map files to convert either .sam or .bed so that I can use them in MACS

[hosang.jeon]

It looks like the path which contains maq2sam command is not in your $PATH.
As you can use samtools, the path where the samtools execution file is located is in your $PATH, but the maq2sam execution file is not in the same directory.
It is in the directory of <DirectoryOfSamtools>/misc.
You can find where your samtools is located using "which samtools" command.

To use maq2sam, you can add the whole path including "misc" to the PATH variable in ~/.bash_profile or ~/.bashrc
After you relogin using user account, you can use maq2sam.
On the other hand, you can use maq2sam by typing command including whole path.

Furthermore, if you're using MAQ version 0.6.X or earlier, you should use command "maq2sam-short". If you're using MAQ version 0.7.X or later, you shoud use command "maq2sam-long"

[vaibhav_jain]

Thanks Hosang.jeon for detailed solution to the problem, I will try to use maq2sam by typing command including whole path.
Do you have any idea if there is any other way to convert .map files to use in MACS ???

Thanks again