I am trying to follow the MiSeqs protocol and have a question. In the SOP it states
mothur > make.contigs(file=stability.files, processors=8)
The first thing you’ll see is that it processes the fastq files to generate the individual fasta and qual files. Then it will go through each set of files and make the contigs
However, i cannot get a quality file from it. I am using the 64 bit version on Windows 7.
Also, lately I have tried downloading and installing the latest version of the Linux 64 bit program (command line). When i click on the download link, for some reason I get version 1.22 instead of 1.32. And the 1.22 version obviously does not contain the make.contigs command for MiSeq.
However, i cannot get a quality file from it. I am using the 64 bit version on Windows 7.
At this time we do not output a consensus quality score file.
Also, lately I have tried downloading and installing the latest version of the Linux 64 bit program (command line). When i click on the download link, for some reason I get version 1.22 instead of 1.32. And the 1.22 version obviously does not contain the make.contigs command for MiSeq.
So we’re actually up to 1.33 :). I suspect the problem is that you have mothur installed somewhere you don’t know. Try running “which mothur” (without the quotes) from the command line. That will tell you where the mothur executable is that you’re trying to run.
At the time I was trying to download it (6/24/2014) that was the version located in the download package for the Linux system.
Since there has been a new version released since then, I will try again.
Regarding the quality file, the wiki is a little confusing in that aspect - at least as i read it.