Hi all 
Sorry in advanced if this is not the right place to ask this question, but I've ran out of ideas.
I have a piece of sequence which I am interested in that I obtained from next-gen data. I took this sequence (a contig of about 2,000 nucleotides long, does not appear repetitive) and BLAT'ed it against canfam3 on UCSC - nothing unexpected, got the correct region. See a bunch of non-refseq genes from humans, and see that the corresponding region in humans is on chromosome 12.
When I take the sequence and BLAT it against the human reference sequence (hg19) I do not get the same regions that I saw previously. I still get a region on chromosome 12 but it is 30 + million bases away from the other.
I have a -feeling- it is because of low conservation, but how can I tell ? In particular, how do I know it is not from misassembly of reference genomes ?
Any ideas would be greatly appreciated. Thanks !
Sorry in advanced if this is not the right place to ask this question, but I've ran out of ideas.
I have a piece of sequence which I am interested in that I obtained from next-gen data. I took this sequence (a contig of about 2,000 nucleotides long, does not appear repetitive) and BLAT'ed it against canfam3 on UCSC - nothing unexpected, got the correct region. See a bunch of non-refseq genes from humans, and see that the corresponding region in humans is on chromosome 12.
When I take the sequence and BLAT it against the human reference sequence (hg19) I do not get the same regions that I saw previously. I still get a region on chromosome 12 but it is 30 + million bases away from the other.
I have a -feeling- it is because of low conservation, but how can I tell ? In particular, how do I know it is not from misassembly of reference genomes ?
Any ideas would be greatly appreciated. Thanks !