TransDecoder in Linux
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4.4 years ago
lexa_2294 • 0

Could you help me convert my nucleotide sequences to amino acids in Linux? I already tried putting:

TransDecoder.LongOrfs -t target_transcripts.fasta

but no results. I'm new to bioinformatics and the command terminal.

PS: I already have the TransDecoder program installed

transdecoder sequence • 2.3k views
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Entering edit mode
4.4 years ago
alex.zaccaron ▴ 450

Looks like you are trying to predict ORFs within assembled transcripts (that is what TransDecoder does). If you successfully ran TransDecoder.LongOrfs -t target_transcripts.fasta, then TransDecoder produces a few files, including longest_orfs.pep which already has the amino acid sequences of the predicted ORFs. But if you just want to translate coding sequences to proteins, use something like EMBOSS transeq.

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