What do "Uu" and "uU" mean in .pairs file?

[jiehua1995]

I found in my mapped.pairs file, mapping status of some lines are uu, uU, Uu. Are they same as UU?

Best,

Jie Hua

[Phlya]

Sorry for the late reply - essentially they are the same. Lowercase pair types indicated that this side contained a chimeric alignment that was rescued, but we decided it was not necessary information and just made everything more complicated. So basically you can consider them the same, if you have files that contain both, but the new versions of pairtools will not report any lowercase pair types.