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Old 01-04-2012, 11:55 AM   #7
Location: cinci

Join Date: Apr 2010
Posts: 66

Originally Posted by ebatis2 View Post

I've received results from my first NGS run and like you posted, I'd like to convert my fastq file to a SAM file in order to upload and retrieve data from Galaxy. I'll need to map the reads and align them to the Rice genome...but is this something I could do on my MacOSX? I'm at a loss as far as how to retrieve the sequencing results! Any help would be greatly appreciated!!
FASTQ is the raw reads with qualities. SAM is format to describe reads and their alignment. This was hinted in the previous respond above. It seems you've got to align the reads first if you just received the raw FASTQ. Perhaps you should be asking how to align your reads. I can't help much because I am not sure what your goal is. Galaxy has a tutorial on how to align your reads and produce a SAM file. Check it out.
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