Hello, good day, sorry for the simplicity but, I have a super basic question. I have been trying to identify the longest ORF of a transcriptome for a long time, but from the previous failed attempts it seems that it is not clear to me how to do it.
You see, I have to make a small ORF (30 to 300 nucleotide ORF) prediction of a transcriptome, but for that, I first need to identify the longest ORF, so what I did was translate the 6 possible reading frames of the transcriptome, to do this used the function transeq from EMBOSS
transeq inputFasta outputFast -frame=6
The above is an example that creates a fasta file with the 6 different reading frames, I did that and also generated a fasta file for each reading frame. Then I made a variety of scripts that did not work to detect the longest ORF in the variety of generated files. If anyone could tell me about some program and function to help me find this longest ORF or give me clues on how to make a proper script, I would greatly appreciate it. Thanks for your time and have a nice day!
How to extract the longest orf?
Is there any script to select longest ORF instead longest transcript from all assembled transcripts by Trinity?