Alignment to selected region of the reference genome

[houkto]

Hi There,

I usually align my NGS reads of rat strains to Brown Norway (rat) reference genome. However, the rat reference genome still a draft and there are many gaps in the genome. Recently, we obtained one of these gaps (3 fasta files) that we are interested in by the group who will release the next assembly. The question now how I can integrate these fasta files (we know the coordinations) into the reference genome .fa file?

Would aligning our reads against these fasta files would subsequently give us the SNPs and Indel of the new fasta files regions or shall the way to do it is by integrating the files into the genome (would like to know how) is the only way to get the variants in the new regions ?

Cheers

[westerman]

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.