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Old 02-17-2012, 10:38 AM   #1
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Location: UK

Join Date: Sep 2011
Posts: 5
Default Alignment to selected region of the reference genome

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 ?

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