I have the sequence for the OP50 strain of E. coli and I would like to compare it to the reference E. coli sequence. Does anybody know how I can do this? I am trying lastz:
lastz chr1.fa ecoli.fa --notransition --step=20 --nogapped --format=maf --rdotplot=rplot.txt > AvsB.maf
However, I do not know how to read the .maf file and the rplot.txt file is empty.
Your help would be appreciated.