Hi, everyone. I will resequence a region. But I have a confusion. In my region, there are many repeat regions(70% of interest region). If I avoid repeat regions, only 30% of all bases will be sequenced, will this affect my result of fine-mapping? Thank you in advance.
Repeat regions are not all created equal, at least when talking about short-read sequencing. You might consider looking at the mappability tracks at UCSC or even simulating some reads in the region to do your own mappability analysis. Otherwise, consider sequencing the region and know that you will probably get more than 30% of the bases but less than 100% after mapping the resulting reads back to the genome.
I like Sean's suggestion. Sequencing the entire region gives you the opportunity to detect variation (single nucleotide, loss, gain) of any of the repeats you have seen in this region. You did not tell us what types of repeats you have here. If these are di- or tri-nucleotide repeats, you definitely want to sequence these as these are much more powerful genetic markers than SNPs - because SNPs are typically bi-allelic and the others often have many alleles.
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How are you going to do the sequencing? What organism are you working with?
human. DNA resequencing(include intron,exon and other regions).
What technology were you going to use to do the sequencing? And how are you going to capture your region of interest?
Illumina HiSeq 2000; Agilent sureselect