What does this code mean when using BBMap?

Question

[camerongubbins5]

I am currently in the Unix environment. I am a little confused about some code I have found when utilising BBMap to translate the nucleotide sequence into protein.

translate6frames.sh in=${inputGeneFasta} out=${outputProtFasta} frames=1

From what I have read the translate6frames part is basically saying translate the nucleotide sequences to all 6 amino acid frames. I was unsure whether the frames=1 is just specifying use only the first reading frame to translate the genes into protein.

Please could somebody specify what frames=1 is and if this is good to use?

Answer 1

[jean.elbers]

./translate6frames.sh 
.....some output not shown
frames=6        Only print this many frames.
            If you already know the sense, set 'frames=3'.
.....some output not shown

It prints 1 frame, presumably the first

[camerongubbins5]

@jean.elbers. Thank you for your reply. Why would it be any better to print only the first frame ( I am assuming the longest open reading frame), versus frames 2, 3 or 4?

[jean.elbers]

Frame 1 is not necessarily the longest open reading frame. It depends on your nucleotide sequences, especially if they are not in fact from coding regions or are pseudogenes. Short answer is it depends on your data. That’s about all that I can say.