I'm using gap5 to analyze my assembly. When I select the template display windows for any contig, I don't see any read pair coloured with grey, most are coloured with red. According to the manual the colors are blue, orange, red and grey, being grey for consistent read pairs. It's impossible that any read pair has been positioned well.
I have two mate libraries,
-Ion torrent Mate pair library with an average size of 8.9 kb with orientation -> ->
-Ion torrent Mate pair library with an average size of 3.5 kb with orientation -> ->
I checked the List of libraries, in the view panel and the information is consistent with my reads.
Is possible that template display recognizes -> -> how an inconsistent orientation?
I say because most of mate pair are in red and, acording the manual, this templates are considered as inconsistent typically due to the relative position and orientation of the forward and reverse sequences being incorrect.
Thanks in advance!
Sorry for my english.
Sorry for the late reply. Sourceforge has oddly stopped emailing me notifications of bugs and discussion comments.
I believe this is fixed in the latest code in CVS, but we really need to produce a proper new release so we can get these fixes out there. Originally it treated everything as "-> <-" for consistent. It now checks the library histogram to see which is the usual orientation for a library and then uses this to work out consistency.
The List Libraries (main view menu) will allow you to see what Gap5 thinks the proper orientation is.