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Old 02-20-2012, 05:51 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

Originally Posted by houkto View Post

Would aligning our reads against these fasta files would subsequently give us the SNPs and Indel of the new fasta files regions ...
It should. Especially if you can eliminate the reads that map to other parts of the reference. You'll probably miss SNP/InDel at the ends of the new sequence (because reads do not map at the end) but depending on the size of your new sequence this may not be significant.

... or shall the way to do it is by integrating the files into the genome (would like to know how) ...
That would work as well. As far as how to do this, I doubt if there are any general tools available. You will probably have to do some cut-and-paste and/or custom programs in order to modify your reference sequence and annotation files. It does not seem that difficult since you know the coordinates.
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