[mira_talk] Re: Solexa paired-end reads
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 1 Mar 2011 21:00:40 +0000
On Tue, Mar 1, 2011 at 7:54 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> 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).
>
> B.
That's great news - feel free to borrow any code ideas, or ask me
for any clarification of how I thought MIRA to SAM should work.
Peter
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