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Old 12-10-2012, 10:00 PM   #8
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Location: Pune, India

Join Date: Dec 2012
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Originally Posted by husamia View Post
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.
I have the raw FASTQ reads and in order to perform de novo assembly using transAbySS, I need to feed the input in the form of bam or sam. Can you please shed some light on this.
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