Actually the manual clearly says that SB is the usual placement for 454. Sorry about that.
On 01/10/12 09:21, Andrej Benjak wrote:
Ups.OK, maybe I know why I got confused. This is from the sff_extract ver 0.3:########################### If the read can be split, two reads will be written. In standard mode,both reads will be in forward direction (as in the sequence form the SFF) and the read names will have /1 and /2 appended. In compatibility mode,the side left of the linker will be named ".r" and will be written inreverse complement into the file to conform with what older assemblers and scaffolders expect when reading paired-end data. The side right of thelinker will be named ".f" ###########################So, the "both reads will be in forward direction" actually means "the directions of reads wont be touched", meaning it will keep as the original 454 orientation, right?Thanx for pointing out that the default 454 segment type is SB!(could be a good idea to put it in the manual maybe, even if it's something with a limited guarantee like "454-Ti is SB, but it's on you to check in case of new chemistries...).Andrej On 01/10/12 08:59, Bastien Chevreux wrote:On Oct 1, 2012, at 8:52 , Andrej Benjak wrote:No particular reason for using "samedir". I wasn't sure what to use with 454 at first, then later on I read the comments in the "sff_extract" and figured it's "SF".Ummm ... what?! There's a comment like this in sff_extract? It must be an old one or I was completely insane when writing that. Indeed, it must be "SB" (or "righties" in bamstat speak).But hey, at least we found a little bug to fix (although certainly not at your amusement, sorry).Only a squashed bug is a good bug :-) B.
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