I should have reviewed about mapper program (maq, bowtie..) earlier. Most of the first step in NGS data analysis is mapping read to reference genome. So knowing this process is prior to the others. But I just do this work now.
Here is the PPT.
ah.. I have to confess that some of slides in PPT come from mqoqol's ppt in SEQanswers.
Thanks mqoqol!
I found a blog today.
http://hackmap.blogspot.com/2010/07/aligners-since-starting-methylcoder.html
In the blog, the owner addressed shortcoming of Bowtie. And he introduced GSNAP. Actually in our firm, we made a tentative arrangement to use GSNAP for aligner.
I will also have to review the paper (GSNAP) ASAP.
