Make Paired File Task-Scripture

Question

[GPR]

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.

Answer 1

[Istvan Albert]

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.

[GPR]

Thanks a lot, I will look into this.