PS: I have posted this to tophat/cufflinks list but unfortunately have not heard back. To be fair to the developer team, some of them might be on affected by Sandy
Briefly what is the policy for cuffmerge when it is trying to merge transcript models from different time points/ conditions when a transcript is only found in 1 or may be 2 of the condition compared to other 7-10 conditions..does it consider it as as artifact or not ?
The reason we are asking this question of the data is to see if there are transcripts in the data which are only found in 1-2 conditions and may just be false. I understand they might be very sepcific to that condition and may be biologically meaningful but for now we are just trying to ascertain how many such transcripts may be there.
I am wondering if cuffmerge keeps such transcripts or gets rid of them in the first place which then will make our exercise moot. I will appreciate a quick response if feasible.