Just a confusion in the wiki page documentation, Step 3: predict the likely coding regions. The information about using the -S flag should be at Step 1: extract the long open reading frames. It is TransDecoder.LongOrfs, not TransDecoder.Predict, that takes this flag.
Just a confusion in the wiki page documentation, Step 3: predict the likely coding regions. The information about using the -S flag should be at Step 1: extract the long open reading frames. It is TransDecoder.LongOrfs, not TransDecoder.Predict, that takes this flag.