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