[mira_talk] Re: Solexa paired-end reads

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 1 Mar 2011 20:54:15 +0100

On Sunday 27 February 2011 19:07:24 Peter wrote:
> [...]
> The details are not fresh to mind, but I think there is some headers
> that can be used in SAM/BAM to give library information like that
> (probably at the read group level). However, for each read pair
> there is a specific field for the insert/template size (one integer),
> which is what I was looking at for now.

Do not put too much work into that ... I just decided today to write a SAM 
exporter. You'll have to thank James Bonfield for that decision ... his newest 
version of gap5 has a CAF importer and a SAM exporter, which enables me to 
have a complete loop to test my code.

Though James and I will have to tackle a few things still (tags come to mind).


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