On Sep 17, 2012, at 20:57 , Laurent MANCHON wrote: >> I suspect your files do not adhere to the above :-) > you are right, this is what i have: > [...] > it seems to be a Casava 1.8 format but pair member is missing Well, renaming the reads to have /1 and /2 will do the trick. a sed one-line should be able to take care of that. B.