Hello, I am trying to prepare the input file for Scripture and have stumbled upon the fact that I need to have the TopHat alignment output split into right and left reads. Can somebody tell me how to do this? I obviously had a bam file,containing both right and left reads. Thanks, G.
I think you could get that information from the SAM file. the spec says that column 8 PNEXT indicates the position of the mate/next segment.
So for each line if the position is larger than the current position then it is a left read otherwise a right read.