[Mac OS X, 10.4.x]
Can someone write an outline (for OS X) of how two related .abi files can be assembled into a contig, and edited (assume a couple of errors over 500-800nt), in 5 minutes or less?
I try and use pregap4 and gap4 every now and then, but I find it very frustrating. In sequencher I can drag a few .abi files together, press the magic button, they align, and I can start editing. In pregap4/gap4 I can spend hours, poring over the manuals, trying to find files through the X11 directory window (a cramped, and very tedious way to locate anything), and may manage to get a couple of sequences overlapped.
a)The X11 file finding window is small and cumbersome
It never remembers the last place you were
b) getting .abi files through pregap4 into gap4 seems almost impossible at times. This shouldn't be so difficult. It either can't make a gap4 database, can't open it or puts nothing in it. Why can't pregap4 finish then offer you the chance to open up the newly created database in gap4 (or some similar, seamless way to get to where you want to be). The file names have to have particular prefixes/suffixes (?), the gap4 assembly can't be used to put things into a gap4 database (?).
I realise this software is very powerful, but in its present form it is so hard to use, even for people like me who are fairly confident with *nix.