Paire-End Alignments And Scripture

Question

[GPR]

Hello, I am slowly getting my hands on Scripture and have stumbled on yet another unclear (at least to me )detail. I have paired-end data and the two pairs are in a sigle TopHat-derived *.bam file. I have walked my way through the Tuxedo protocol and didn't need two files per paired-end alignment in Cufflinks or Cuffdiff. My question regarding Scripture is: How do I do I input my alignment file in the "makePairedFile" step?. So far I sorted by queryname with Picard and removed the headers with "sed '1,2d'. Given that I have a single file already, should I jump directly to sort/index with igvtools and then run Scripture with the flag -pairedEnd instead of alignment?

Help will be appreciated. G.