If you've ever wondered how mappable a specific repeat is, here's a quick post on creating a plot showing the mappability of a repetitive element along its consensus sequence. Specifically, the consensus sequence of a repeat was taken and sub-sequences were created by a sliding window approach (i.e. moving along the sequence) at 1 bp intervals and these sub-sequences were mapped to hg19.
I will use bwa for the mapping, so firstly download and compile bwa:
wget http://sourceforge.net/projects/bio-bwa/files/latest/bwa-0.7.7.tar.bz2 tar -xjf bwa-0.7.7.tar.bz2 cd bwa-0.7.7 make #index hg19 bwa index hg19.fa