[mira_talk] Re: Solexa paired-end reads
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 27 Feb 2011 16:59:03 +0100
On Friday 25 February 2011 16:05:57 Peter wrote:
> What I need to know is if MIRA was happy with the pair - which I
> could guess from their placement
Hmmm ... if placed within a contig, MIRA is happy with it (if it was asked to
take template info into account).
> 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?
Interestingly ... no. I suppose I'll need to consider that also when reworking
MAF
> 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.
I'm probably not the best informed and knowledgeable person to say this, but
not the first either: SAM/BAM has a number of design flaws which make it, uh,
not ideally suited for every use case. However, I think that in just this case
there may be a workaround: doesn't SAM have some sort of library information
field which defines average insert size of a lib and stdev?
B.
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