paired-end and Scripture

[EBER]

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.

[Chirag]

Hey EBER,
Did u manage to solve it ?
As tophat takes both pair-ends at the same time, some of the steps mentioned in the walkthrough are not necessary, and kinda makes confusing. Any help will be appreciated.

cheers

[Yt Shen]

Hi Chirag,
Did you find something interesting for scripture? I mean that protocols about makepairedEnd. Does scripture can use the pair-end reads directly?

Any help will be appreciate

[Chirag]

I think i merged all the bam files (combine all replicates and stages), and ran the scripture. Was fine, comparable to Cufflinks.

[Yt Shen]

Dear Chirag,

If I want to ananlysis the AS event in each sample,also I need merge all the .bam file together?