paired-end and Scripture

EBER · 07-25-2012, 07:13 AM

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 · 10-08-2012, 03:57 AM

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 · 12-09-2012, 05:41 PM

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 · 12-10-2012, 02:09 AM

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

Yt Shen · 12-10-2012, 06:59 PM

Dear Chirag,

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

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07-25-2012, 07:13 AM	#1
EBER Member Location: New Haven, CT Join Date: May 2012 Posts: 10	paired-end and Scripture 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.

10-08-2012, 03:57 AM	#2
Chirag Member Location: Norway Join Date: Nov 2011 Posts: 23	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

12-09-2012, 05:41 PM	#3
Yt Shen Junior Member Location: Beijing,China Join Date: Oct 2012 Posts: 3	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

12-10-2012, 02:09 AM	#4
Chirag Member Location: Norway Join Date: Nov 2011 Posts: 23	I think i merged all the bam files (combine all replicates and stages), and ran the scripture. Was fine, comparable to Cufflinks.

12-10-2012, 06:59 PM	#5
Yt Shen Junior Member Location: Beijing,China Join Date: Oct 2012 Posts: 3	Dear Chirag, If I want to ananlysis the AS event in each sample,also I need merge all the .bam file together?