confusing SNAP output
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5.8 years ago
amoltej ▴ 90

Hi ALL,,

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.

Amol

SNAP Annotation Assembly ZFF • 1.7k views
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