Hello Biostars community,
I have generated bed file from chip-seq experiment and would like to filter my mutations that occurred in these regions with bed file input. But I have found less mutations than I expected.
My initial guess is increasing the peak with by 500 bp from both sides but I have a concern before I conduct this step. I dont know if -500 from start and +500 to end will work because what if a peak is at the edge of a chromosome. Therefore, could someone illuminate me about the positions of the chromosomes?
1) Does grch37 assembly start from 0 and continuously go until the end of mitochondrial genome ? or 2) for each chromosome it starts from 0 and end some where and for the next chromosome it starts from the beginning?
I know this is a very fundemental question but sometimes we do complicated work and forget about this basic stuff.
Thank you for the help,