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Macki1x 08-09-2008 11:35 AM

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.

ECO 08-09-2008 01:00 PM

Hey there...I would suspect that the "FASTQ" file you have is really solexa's format that is off just a bit. There are some notes on the conversion here:

http://maq.sourceforge.net/fastq.shtml

I think there is a script included sol2sanger.pl that will do that change for you...otherwise someone else will have to jump in.

apfejes 08-11-2008 10:49 AM

Just a late note, and somewhat off topic, but might be of interest to users of old macs...

I believe the .map files created by maq use the little-endian/big-endian-ness of the platform being used - that is to say the order of the bits may change in the binary file depending on the native format of the processor being used. This could be a problem for converting between a powerPC processor and an Intel x86 based processor. You may have to convert to mapview format using the same computer as where the alignment was done to transfer information between them.

Since the vast majority of hardware is x86 based these days, I doubt this is a problem, but maybe worth mentioning here so that there's some reference for it.

Cheers.

Note: I'm not a developer for MAQ, and only know anything about the MAQ .map format from reading the source code and implementing a .map file parser. Please contact your local MAQ expert for more information, or feel free to read the source code yourself! (=


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