Thread: maq on a mac
View Single Post
Old 08-09-2008, 10:35 AM   #1
Macki1x
Junior Member
 
Location: usa

Join Date: Dec 2007
Posts: 5
Default maq on a mac

Hello,

I have downloaded my first solexa 1g sage data set in fastq format from a collaborator with a 1G machine (1.9GB) and wish to analyze it.

They recommended maq, and I downloaded maq from sourceforge. I would like to start my analysis by running easyrun using my sage data set (which I named cd1.fastq) against the reference mouse chromosome 1 in fasta format (which I named 1.fasta) as a start.

I am trying to do this on a mac g4 (using terminal). I created a folder (/../../Maq/maq-darwin) containing maq, maq.pl, the fastq file (cd1.fastq) and the reference file (1.fasta).

When I execute easyrun (perl maq.pl easyrun 1.fasta cd1.fastq), an easyrun folder is created and an alias (ref.bfa) is created, then

The program very quickly stops running and I get this error:

** Cannot guess the format of file '/../../Maq/maq-darwin/cd1.fastq'. at maq.pl line 107.

I am new to bioinformatics and fairly naive regarding sequnce analysis and I would gratefully appreciate any comments or ideas as to why my fastq file (cd1.fastq) is not recognized and how I can analyze my data set.

Thank you very much for any suggestions or explanations.
Macki1x is offline   Reply With Quote