TransDecoder in Linux
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
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lexa_2294 •
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lexa_2294 •
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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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