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Transdecoder producing more proteins than assembly

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?

rna-seq
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updated by h.mon h.mon • written by 1234anjalianjali1234 • 1234anjalianjali1234

Using all reading frames?

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written by GenoMax GenoMax

1 answer

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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written by h.mon h.mon

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