[mira_talk] Re: Solexa paired-end reads
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 25 Feb 2011 15:05:57 +0000
On Thu, Feb 24, 2011 at 8:33 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Thursday 24 February 2011 13:08:57 Peter wrote:
>> Then the question becomes how to set that bit when generating
>> the SAM file from MAF... perhaps Bastien has some ideas?
>
> Bastien is currently swamped by some Solexa sequencing projects in the 50 to
> 100m range and has had some interesting weeks and sleep-deprived nights in
> getting MIRA up to speed for those.
What I need to know is if MIRA was happy with the pair - which I
could guess from their placement but I won't know if the directionality
is expected to be --><-- (classical Sanger pairs), <-- --> (mate pairs?),
or potentially --> --> (PacBio? or if you change things, Roche 454).
Does the MAF file indicate the -GE:tpbd=1 or -GE:tpbd=-1 setting
in any way?
---
Also, Tony was asking for insert sizes. I see the MAF file can contain
the following lines for a read:
TF integer: template size from
Minimum estimated size of a sequencing template. In paired-end
sequencing, this is the minimum distance of the read pair.
and:
TT integer: template size to
Maximum estimated size of a sequencing template. In paired-end
sequencing, this is the maximum distance of the read pair.
Sadly for SAM/BAM we just get one number for the estimated
template size (insert size). When the two reads are used in the
same contig, I could infer the template length from their placement.
> SAM/BAM is currently very far down my priority list, but ... have you thought
> of a multiple parsing strategy of the MAF file? In the first pass collect the
> data you need for the second pass?
I'm considering it, yes.
Peter
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
