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?
Using all reading frames?
Yes... With default parameter.
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).
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