6.8 years ago by
I got my answer. Below is the graphic ideograms of Mouse karyotypes from Ensembl.
So, the start of each chromosome in UCSC is the centromere, which can span to first ~3M bases. There are no genes in the region, the second screenshot of Chr2 in Mouse. I've checked a couple of others as well.
So, if anything binding there, might be noise. Centromeres and Telomeres are contituting a lot of repetitive regions as well, which I generally remove, thus no mapping observed.
Can someone comment on how can we pull this information from the databases (UCSC), how much region in spanned to Centrosome/Telomere and contains no genes, one useful case would be on how to modify the chromosome co-cordinate file, so as to replace the start
0 with position where centromere ends. This file has a usecae with the BEDOPS-based binning script to calculate the coverage, thus will save little time and resources.