I was using SNAP annotation pipeline for prediction. those who have used it might know that it needs ZFF file. So I have got two scripts to make this ZFF file. one is from Maker software and one is from SNAP author Dr. Ian Korf. After running snap I find out that the total number of predicted transcripts using maker gff2zff.pl gives me more than 80k transcripts which is unusual. while when I used authors script to make ZFF file it gave me about predicted 18K transcripts. This number is OK but when I look closely I found out the largest scaffold in my genome showing only two genes which are abnormally big.
can anyone tell me what might be the problem? How should I proceed?
Thank you in advance.