I'm trying to make a method in order to generate an proximate alignment among two whole mammalian genomes in quick time. At the moment in order to evaluate my results I want to convert my output into psl format.
My problem is that I cannot understand the way of the calculation of the qstarts and tstarts values (the two last values) for the negative strand. At the positive strand, the qstarts will be the same with starting position at the query and the tstarts will be the starting position of the target.
For the negative strand, if you will see the following example:
132 22 0 0 0 0 0 0 - chr24 61756751 49146459 49146613 chr22 61598339 1042089 1042243 1 154, 12610138, 1042089,
how are being calculated the last two numbers?
Thank you very much in advance,