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Published 20 hours ago • verified publisher icon Gaius-Augustus

blat2hint.pl

Open chiu-shenpo opened this issue 3 years ago • 1 comments

I have used e-training to establish my own species model. However, according to the manual "Incorporating RNA-Seq into AUGUSTUS", it uses blat2hints.pl getting the information of intron. I don't know how blat2hint2.pl works? (How does it find the position of intron?????) I felt like the whole hint file thing is kind of overlapping if I already e-trained my own species model by PASA and Transdecoder.

chiu-shenpo avatar May 12 '21 02:05 chiu-shenpo

Please have a look at these instructions: https://math-inf.uni-greifswald.de/storages/uni-greifswald/fakultaet/mnf/mathinf/stanke/augustus_wrp.pdf

You want to predict genes as accurately as possible. Therefore, it is ok to train your gene finder on information that is highly reliable, and also use that same reliable information during gene prediction.

KatharinaHoff avatar May 21 '21 14:05 KatharinaHoff