Hi, I mapped next-generation sequencing data of a dog genome to the dog reference genome (canFam2), and search for the SNP and indel. But I found that some SNPs and indels are due to the mistakes in dog reference genome, which are different from the human or mouse genome. For example:
I found a indel of my input dog genome by comparing the canFam2 reference genome, and the reference is T in this base pair region, but the input has one base pair deletion in this region: chr38:8,242,507-8,242,507 T - However, I found that the human, mouse and rat have no T in this base pair from conservation in browser. So there may be a mistake in this base pair region of canFam2 reference genome. Now I want search for all my SNP and indel results back to the canFam2 reference genome, and find out which are the real changes, and which are due to the canFam2 reference mistake by comparing the dog to the human and mouse genomes. And I download the multiple alignments files from dog canFam2, but it is very hard to output all the possible mistakes related to my SNP and indel regions. So is it possible I can get the conservation from some specific regions (my SNP and indel)? Thanks a lot. -- Deli Liu Institute of Bioinformatics, University of Georgia Athens, GA, 30605 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
