TransDecoder in Linux

Question

[lexa_2294]

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

Answer 1

[alex.zaccaron]

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.