How to Count - Part Deux
I described a method for counting mismatches previously. This time, I'll count something different in a slightly different manner, but the principles will be the same. In this case, we're looking for mismatches to the official genome in sequence reads, but we want to know how the mismatch rate varies along the read. The position along the read is called the cycle , because it indicates the machine cycle that sequenced the particular base. The basic method is similar to the one used in the previous post, but this time we'll use perl instead of python. Perl receives a lot of bad press these days, having gone from the being the Swiss-army chainsaw of the web to having its web processing thunder stolen by Php and its general programming ubiquity being usurped by python. Still, I like perl and use it frequently. Perhaps, this is because I have been using it for so long that I know many of its idiosyncrasies and can either workaround them or use them to my advantage. Despite...