Transdecoder producing more proteins than assembly

Question

[1234anjalianjali1234]

While using transdecoder ( TransDecoder.LongOrfs option), I am getting proteins more than the number of sequences in my assembly. Is this usual to get this kind of result?

[GenoMax]

Using all reading frames?

[1234anjalianjali1234]

Yes... With default parameter.

Answer 1

[h.mon]

TransDecoder.LongOrfs is just an intermediary step on the TransDecoder pipeline. To get the final set of predicted proteins, one has to run TransDecoder.Predict (after possibly running HMMER and Blast+ on the peptides from TransDecoder.LongOrfs).