Question

Transdecoder producing more proteins than assembly

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2.7 years ago

1234anjalianjali1234 ▴ 40

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 • 944 views

ADD COMMENT • link updated 2.7 years ago by h.mon 34k • written 2.7 years ago by 1234anjalianjali1234 ▴ 40

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Using all reading frames?

ADD REPLY • link 2.7 years ago by GenoMax 119k

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Yes... With default parameter.

ADD REPLY • link 2.7 years ago by 1234anjalianjali1234 ▴ 40

score 0 · Answer 1 · 2019-12-12

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2.7 years ago

h.mon 34k

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).

ADD COMMENT • link 2.7 years ago by h.mon 34k